Modified coagulation factor IX polypeptides and use thereof for treatment

ABSTRACT

Provided are modified factor IX (FIX) polypeptides and methods of generating modified FIX polypeptides. Also provided are pharmaceutical compositions, including compositions formulation for oral administration, that contain the modified FIX polypeptides, and methods of treatment using modified FIX polypeptides.

RELATED APPLICATIONS

This application is a continuation of now allowed co-pending U.S. application Ser. No. 11/818,985, entitled “MODIFIED COAGULATION FACTOR IX POLYPEPTIDES AND USE THEREOF FOR TREATMENT,” to Jorge Oyhenart, Xavier Gallet, Gilles Borelly, Thierry Guyon, Manuel Vega and Lila Drittanti, filed Jun. 15, 2007, which claims priority under 35 U.S.C. §119(e) to U.S. Provisional Application Ser. No. 60/815,113, entitled “MODIFIED COAGULATION FACTOR IX POLYPEPTIDES AND USE THEREOF FOR TREATMENT,” to Jorge Oyhenart, Xavier Gallet, Gilles Borelly, Thierry Guyon, Lila Drittanti and Manuel Vega, filed Jun. 19, 2006.

This application is related to International Application Serial No. PCT/US2007/14219, entitled “MODIFIED COAGULATION FACTOR IX POLYPEPTIDES AND USE THEREOF FOR TREATMENT,” which also claims priority to U.S. Provisional Application Ser. No. 60/815,113. The subject matter of each of these applications is incorporated by reference in its entirety.

This application is also related to U.S. application Ser. No. 11/176,830, to Rene Gantier, Thierry Guyon, Manuel Vega and Lila Drittanti, entitled “RATIONAL EVOLUTION OF CYTOKINES FOR HIGHER STABILITY, THE CYTOKINES AND ENCODING NUCLEIC ACID MOLECULES,” filed Jul. 6, 2005 and published as U.S. Application No. US 2006-0020116, which is a continuation of U.S. application Ser. No. 10/658,834, to Rene Gantier, Thierry Guyon, Manuel Vega and Lila Drittanti entitled “RATIONAL EVOLUTION OF CYTOKINES FOR HIGHER STABILITY, THE CYTOKINES AND ENCODING NUCLEIC ACID MOLECULES,” filed Sep. 8, 2003 and published as U.S. Application No. US-2004-0132977-A1. This application also is related to U.S. application Ser. No. 11/196,067, to Rene Gantier, Thierry Guyon, Hugo Cruz Ramos, Manuel Vega and Lila Drittanti entitled “RATIONAL DIRECTED PROTEIN EVOLUTION USING TWO-DIMENSIONAL RATIONAL MUTAGENESIS SCANNING,” filed Aug. 2, 2005 and published as U.S. Application No. US-2006-0020396-A1, which is a continuation of U.S. application Ser. No. 10/658,355, to Rene Gantier, Thierry Guyon, Hugo Cruz Ramos, Manuel Vega and Lila Drittanti entitled “RATIONAL DIRECTED PROTEIN EVOLUTION USING TWO-DIMENSIONAL RATIONAL MUTAGENESIS SCANNING”, filed Sep. 8, 2003 and published as U.S. Application No. US 2005-0202438.

This application also is related to U.S. application Ser. No. 10/658,834, filed Sep. 8, 2003, and to published International PCT Application WO 2004/022593, to Rene Gantier, Thierry Guyon, Manuel Vega and Lila Drittanti entitled, “RATIONAL EVOLUTION OF CYTOKINES FOR HIGHER STABILITY, THE CYTOKINES AND ENCODING NUCLEIC ACID MOLECULES.” This application also is related to U.S. application Ser. No. 10/658,355, filed Sep. 8, 2003, and to International PCT Application WO 2004/022747, to Rene Gantier, Thierry Guyon, Hugo Cruz Ramos, Manuel Vega and Lila Drittanti entitled “RATIONAL DIRECTED PROTEIN EVOLUTION USING TWO-DIMENSIONAL RATIONAL MUTAGENESIS SCANNING.”

Where permitted the subject matter of each of the above-referenced applications is incorporated by reference in its entirety.

INCORPORATION BY REFERENCE OF SEQUENCE LISTING PROVIDED ON COMPACT DISCS

An electronic version on compact disc (CD-R) of the Sequence Listing is filed herewith in duplicate (labeled Copy #1 and Copy #2), the contents of which are incorporated by reference in their entirety. The computer-readable file on each of the aforementioned compact discs, created on Nov. 13, 2012, is identical, 6,982 kilobytes in size, and titled 4930Bseq.001.txt.

FIELD OF INVENTION

Modified coagulation factor IX (factor IX; FIX; F9) polypeptides are provided. The FIX polypeptides are modified to exhibit physical properties and activities that differ from unmodified and wild-type FIX polypeptides. Nucleic acid molecules encoding these polypeptides also are provided. Also provided are methods of treatment and diagnosis using the modified FIX polypeptides.

BACKGROUND

Effective delivery of therapeutic proteins for clinical use is a major challenge to pharmaceutical science. Once in the blood stream, these proteins are constantly eliminated from circulation within a short time by different physiological processes, involving metabolism as well as clearance using normal pathways for protein elimination, such as (glomerular) filtration in the kidneys or proteolysis in blood. Once in the luminal gastrointestinal tract, these proteins are constantly digested by luminal proteases. The latter can be a limiting process affecting the half-life of proteins used as therapeutic agents in per-oral administration and either intravenous or intramuscular injection. The problems associated with these routes of administration of proteins are known and various strategies have been used in attempts to solve them.

A protein family that has been the focus of clinical work and effort to improve its administration and bio-assimilation is the blood coagulation factor family, which includes procoagulation factors, such as factor IX (FIX) and factor VIII (FVIII). Deficiencies in the levels of functional coagulation pathway proteins can cause mild to severe bleeding disorders. For example, hemophilia A and B are inherited diseases characterized by deficiencies in FVIII and FIX polypeptides, respectively. The underlying cause of the deficiencies is frequently the result of mutations in FVIII and FIX genes, both of which are located on the X chromosome. Traditional therapy for hemophilias often involves intravenous administration of pooled plasma or semi-purified coagulation factors from normal individuals. These preparations can be contaminated by pathogenic agents or viruses, such as infectious prions, HIV, parvovirus, hepatitis A, and hepatitis C. Hence, there is an urgent need for therapeutic agents that do not require the use of human serum.

Recombinantly produced FIX polypeptides have been approved for procoagulation treatment of hemophilia. Also of therapeutic interest are FIX polypeptides that lack peptidase activity and can have anticoagulant activities useful in the treatment of thrombolytic diseases. Hence, FIX along with other coagulation factors are important therapeutic agents for procoagulant and anticoagulation therapies. Since naturally occurring variants can have undesirable side effects as well as the problems of administration, bioavailability, and short half-life, there is a need to improve properties of FIX for its use as a biotherapeutic agent. Therefore, among the objects herein, it is an object to provide modified FIX polypeptides that have improved therapeutic properties.

SUMMARY

Provided herein are modified Factor IX (FIX) polypeptides that exhibit increased protein stability compared to an unmodified FIX polypeptide. The modified FIX polypeptides provided herein are mutant variants of FIX that display improved protein stability. Modified FIX polypeptides provided herein exhibiting increased protein stability display increased protein half-life in vivo or in vitro compared to an unmodified FIX polypeptide. For example, modified FIX polypeptides provided herein exhibit increased stability in the bloodstream, following oral administration, and/or under storage conditions. Increased protein stability of a modified FIX provided herein can be manifested as increased resistance to digestion by proteases. Such increased stability includes stability as assessed by resistance to blood, intestinal or any other proteases.

Provided herein are modified FIX polypeptides containing one or more amino acid modifications corresponding to amino acid positions E36, R37, T39, E40, S61, S68, E70, P74, K80, D85, T87, S102, E119, K122, E125, P126, P129, R134, S136, T144, E147, P151, D166, T169, S171, T172, S174, D177, E224, T225, T241, E242, T244, K247, E294, T371, E372, and L414 of a mature FIX polypeptide set forth in SEQ ID NO: 2 or 1035. For example, amino acid replacements at any one of the one or more amino acid positions can include replacements of any of E36Q, E36H, E36N, R37H, R37Q, T39Q, T39H, T39N, E40Q, E40H, E40N, S61Q, S61H, S61N, S68Q, S68H, S68N, E70Q, E70H, E70N, P74A, P74S, K80N, K80Q, D85N, D85Q, T87Q, T87H, T87N, S102Q, S102H, S102N, K122N, K122Q, E125Q, E125H, E125N, P126A, P126S, P129A, P129S, R134H, R134Q, S136Q, S136H, S136N, S138Q, T144Q, T144H, T144N, E147Q, E147H, E147N, P151A, P151S, D166N, D166Q, T169Q, T169H, T169N, S171Q, S171H, S171N, T172Q, T172H, T172N, S174Q, S174H, S174N, D177N, D177Q, E224Q, E224H, E224N, T225Q, T225H, T225N, T241Q, T241H, T241N, E242Q, E242H, E242N, T244Q, T244H, T244N, K247N, K247Q, E294Q, E294H, E294N, T371Q, T371H, T371N, E372Q, E372H, E372N, L414I, and L414V of a mature FIX polypeptide set forth in SEQ ID NO: 2 or 1035.

Provided herein are modified FIX polypeptides containing one or more amino acid modifications corresponding to any of FIX polypeptides with modifications corresponding to Y1I, S3Q, S3H, S3N, G4Q, G4H, G4N, K5N, K5Q, L6I, L6V, E7Q, E7H, E7N, E8Q, E8H, E8N, F9V, E15Q, E15N, R16H, R16Q, E17H, E17N, E20Q, E20H, E20N, E21Q, E21H, E21N, K22N, K22Q, S24Q, S24N, F25V, E26H, E26N, E27Q, E27N, R29H, E30Q, E30N, F321, F32V, T35Q, T35H, T35N, T38Q, T38H, T38N, F41I, K43N, K43Q, Y45I, D47Q, G48Q, G48H, G48N, D49N, E52Q, E52H, E52N, S53Q, S53N, L57V, N58Q, N58S, G59Q, G59H, G59N, G60Q, G60N, K63N, K63Q, D64Q, D65N, D65Q, Y69I, F751, F75V, G76Q, G76H, G76N, F77I, F77V, E78Q, E78H, E78N, G79Q, G79H, G79N, E83Q, E83H, E83N, L84I, L84V, K91N, K91Q, N92Q, R94H, R94Q, E96Q, E96H, E96N, F981, F98V, K100N, K100Q, D104N, D104Q, K106N, K106Q, S110Q, S110H, S110N, T112Q, T112H, T112N, E113Q, E113N, Y115I, R116H, R116Q, L117I, L117V, E119Q, E119H, E119N, S123Q, S123N, A127Q, A127H, A127N, P131A, G133Q, G133H, G133N, S138N, T140Q, T140N, S141Q, S141H, S141N, K142N, K142Q, R145Q, A146Q, A146H, A146N, T148Q, T148N, D152N, D152Q, D154N, Y155I, S158H, S158N, T159Q, T159H, T159N, E160Q, E160H, E160N, E162Q, E162H, E162N, T163Q, T163H, T163N, L165I, L165V, F175I, F175V, F178I, F178V, T179Q, T179H, T179N, E185Q, E185N, D186N, D186Q, K188N, K188Q, P189A, P189S, F192I, P193A, W194I, L198V, N199Q, G200Q, G200H, G200N, D203N, D203Q, F205I, G207Q, G207H, G207N, S209Q, S209H, S209N, E213Q, E213N, K214N, K214Q, T218Q, T218H, T218N, A219Q, A219N, A220Q, A220H, A220N, G226Q, G226H, G226N, K228N, K228Q, T230Q, T230H, T230N, E239Q, E239H, E239N, E240Q, E240N, E245Q, E245H, E245N, R248H, R252H, R252Q, P255A, P255S, Y259I, K265N, K265Q, Y266I, L272I, L272V, E274Q, E274H, E274N, L275I, L275V, D276N, D276Q, E277Q, E277H, E277N, P278A, P278S, S283Q, S283H, S283N, Y284I, T286Q, T286H, T286N, P287A, P287S, D292N, D292Q, K293N, K293Q, Y295I, T296Q, T296H, T296N, F299I, K301N, K301Q, F302I, F302V, G303Q, G303N, S304Q, S304H, S304N, Y306I, S308Q, S308H, G309Q, G309H, G309N, G311Q, G311N, R312H, R312Q, F314V, K316N, K316Q, R318H, R318Q, L321I, L321V, Y325I, R327H, R327Q, P329A, P329S, D332N, D332Q, T335Q, T335H, T335N, L337V, R338H, R338Q, S339Q, S339H, S339N, T340Q, T340H, T340N, K341Q, F342I, F342V, T343Q, T343H, T343N, Y345I, F349V, G352Q, G352H, G352N, F353V, G363Q, G363H, G363N, D364Q, S365Q, S365H, G366Q, G366H, G366N, G367Q, G367H, G367N, P368A, E374Q, E374H, E374N, G375Q, G375N, T376Q, T376H, S377Q, S377H, S377N, F378I, L379V, T380Q, T380H, T380N, S384Q, S384H, G386Q, G386H, G386N, E387Q, E387N, M391V, K392N, K392Q, K394Q, Y395I, G396Q, G396H, G396N, I397Q, I397H, I397N, Y398I, T399Q, T399H, K400Q, S402Q, S402H, S402N, R403H, Y404I, K409N, K409Q, E410Q, E410N, K411N, K411 Q, T412Q, T412H, T412N, K413N, K413 Q, T415 Q, T415H, and T415N of the mature FIX polypeptide set forth in SEQ ID NO: 2 or 1035. In a particular example, the modifications in FIX polypeptide are any of T163N, T163H, I164N, I164Q, L165I, I168N, I168H, T169N, T169Q, T169H, S171N, S171Q, S171H, T172Q, T172H, S174N, S174Q, S174H, F175I, T179N, T179Q, T179H, D203Q, and D203N of the mature FIX polypeptide set forth in SEQ ID NO: 2 or 1035. In another example, the modifications in FIX polypeptide are any of D152Q, D154N, T163H, I164Q, I164H, D166Q, D166N, I168Q, I168H, T169H, S171N, S171Q, T172Q, S174Q, S174H, F175H, D177Q, D177N, T179N, T179Q, T179H, T179N, T179Q, T179H, V181Q, V182N, G184N, D186Q, D186N, A187Q, F192I, V197H, L198I, L198V, D203Q, and D203N of the mature FIX polypeptide set forth in SEQ ID NO: 2 or 1035. In yet another example, the modifications in FIX polypeptide are any of T163H, I164Q, I168H, I169H, S171N, S171Q, T172Q, S174Q, S174H, T179N, T179Q, T179H, D203Q, and D203N of the mature FIX polypeptide set forth in SEQ ID NO: 2 or 1035.

Provided herein are modified FIX polypeptides containing two or more amino acid modifications corresponding to modifications at any two or more positions of Y1, S3, G4, K5, L6, E7, E8, F9, V10, G12, L14, E15, R16, E17, M19, E20, E21, K22, S24, F25, E26, E27, A28, R29, E30, V31, F32, E33, T35, E36, R37, T38, T39, E40, F41, W42, K43, Y45, V46, D47, G48, D49, E52, S53, P55, L57, N58, G59, G60, S61, K63, D64, D65, I66, S68, Y69, E70, W72, P74, F75, G76, F77, E78, G79, K80, E83, L84, D85, V86, T87, I90, K91, N92, G93, R94, E96, F98, K100, S102, A103, D104, K106, V107, V108, S110, T112, E113, G114, Y115, R116, L117, A118, E119, K122, S123, E125, P126, A127, V128, P129, P131, G133, R134, V135, S136, V137, S138, T140, S141, K142, L143, T144, R145, A146, E147, T148, V149, P151, D152, V153, D154, Y155, V156, S158, T159, E160, A161, E162, T163, I164, L165, D166, I168, T169, S171, T172, S174, F175, D177, F178, T179, R180, V181, V182, G183, G184, E185, D186, A187, K188, P189, G190, F192, P193, W194, V196, V197, L198, N199, G200, K201, V202, D203, A204, F205, G207, G208, S209, I210, V211, E213, K214, W215, I216, V217, T218, A219, A220, V223, E224, T225, G226, V227, K228, I229, T230, V231, V232, A233, G234, E235, I238, E239, E240, T241, E242, T244, E245, K247, R248, V250, I251, R252, I253, I254, P255, Y259, A261, A262, I263, K265, Y266, D269, I270, A271, L272, L273, E274, L275, D276, E277, P278, L279, V280, L281, S283, Y284, V285, T286, P287, I288, I290, A291, D292, K293, E294, Y295, T296, I298, F299, L300, K301, F302, G303, S304, G305, Y306, V307, S308, G309, W310, G311, R312, V313, F314, K316, G317, R318, S319, A320, L321, V322, L323, Y325, L326, R327, V328, P329, L330, V331, D332, R333, A334, T335, L337, R338, S339, T340, K341, F342, T343, I344, Y345, M348, F349, A351, G352, F353, E355, G356, G357, R358, D359, S360, G363, D364, S365, G366, G367, P368, V370, T371, E372, V373, E374, G375, T376, S377, F378, L379, T380, G381, I382, I383, S384, W385, G386, E387, E388, A390, M391, K392, G393, K394, Y395, G396, I397, Y398, T399, K400, V401, S402, R403, Y404, V405, W407, I408, K409, E410, K411, T412, K413, L414, and T415 of a mature FIX polypeptide set forth in SEQ ID NO: 2 or 1035. For example, amino acid amino acid replacements at any two or more of the amino acid positions can include replacements of any of Y1H, Y1I, S3Q, S3H, S3N, G4Q, G4H, G4N, K5N, K5Q, L6I, L6V, E7Q, E7H, E7N, E8Q, E8H, E8N, F9I, F9V, V10Q, V10H, V10N, G12Q, G12H, G12N, L141, L14V, E15Q, E15H, E15N, R16H, R16Q, E17Q, E17H, E17N, M191, M19V, E20Q, E20H, E20N, E21Q, E21H, E21N, K22N, K22Q, S24Q, S24H, S24N, F25I, F25V, E26Q, E26H, E26N, E27Q, E27H, E27N, A28Q, A28H, A28N, R29H, R29Q, E30Q, E30H, E30N, V31Q, V31H, V31N, F32I, F32V, E33Q, E33H, E33N, T35Q, T35H, T35N, E36Q, E36H, E36N, R37H, R37Q, T38Q, T38H, T38N, T39Q, T39H, T39N, E40Q, E40H, E40N, F41I, F41V, W42S, W42H, K43N, K43Q, Y45H, Y45I, V46Q, V46H, V46N, D47N, D47Q, G48Q, G48H, G48N, D49N, D49Q, E52Q, E52H, E52N, S53Q, S53H, S53N, P55A, P55S, L571, L57V, N58Q, N58S, G59Q, G59H, G59N, G60Q, G60H, G60N, S61Q, S61H, S61N, K63N, K63Q, D64N, D64Q, D65N, D65Q, 166Q, 166H, 166N, S68Q, S68H, S68N, Y69H, Y69I, E70Q, E70H, E70N, W72S, W72H, P74A, P74S, F75I, F75V, G76Q, G76H, G76N, F77I, F77V, E78Q, E78H, E78N, G79Q, G79H, G79N, K80N, K80Q, E83Q, E83H, E83N, L84I, L84V, D85N, D85Q, V86Q, V86H, V86N, T87Q, T87H, T87N, 190Q, 190H, 190N, K91N, K91Q, N92Q, N92S, G93Q, G93H, G93N, R94H, R94Q, E96Q, E96H, E96N, F981, F98V, K100N, K100Q, S102Q, S102H, S102N, A103Q, A103H, A103N, D104N, D104Q, K106N, K106Q, V107Q, V107H, V107N, V108Q, V108H, V108N, S110Q, S110H, S110N, T112Q, T112H, T112N, E113Q, E113H, E113N, G114Q, G114H, G114N, Y115H, Y115I, R116H, R116Q, L117I, L117V, A118Q, A118H, A118N, E119Q, E119H, E119N, K122N, K122Q, S123Q, S123H, S123N, E125Q, E125H, E125N, P126A, P126S, A127Q, A127H, A127N, V128Q, V128H, V128N, P129A, P129S, P131A, P131S, G133Q, G133H, G133N, R134H, R134Q, V135Q, V135H, V135N, S136Q, S136H, S136N, V137Q, V137H, V137N, S138Q, S138H, S138N, T140Q, T140H, T140N, S141Q, S141H, S141N, K142N, K142Q, L143I, L143V, T144Q, T144H, T144N, R145H, R145Q, A146Q, A146H, A146N, E147Q, E147H, E147N, T148Q, T148H, T148N, V149Q, V149H, V149N, P151A, P151S, D152N, D152Q, V153Q, V153H, V153N, D154N, D154Q, Y155H, Y155I, V156Q, V156H, V156N, S158Q, S158H, S158N, T159Q, T159H, T159N, E160Q, E160H, E160N, A161Q, A161H, A161N, E162Q, E162H, E162N, T163Q, T163H, T163N, I164Q, I164H, I164N, L165I, L165V, L165Q, L165H, D166N, D166Q, I168Q, I168H, I168N, T169Q, T169H, T169N, S171Q, S171H, S171N, T172Q, T172H, T172N, S174Q, S174H, S174N, F175I, F175V, F175H, D177N, D177Q, F178I, F178V, F178H, T179Q, T179H, T179N, R180H, R180Q, V181Q, V181H, V181N, V182Q, V182H, V182N, G183Q, G183H, G183N, G184Q, G184H, G184N, E185Q, E185H, E185N, D186N, D186Q, A187Q, A187H, A187N, K188N, K188Q, P189A, P189S, G190Q, G190H, G190N, F192I, F192V, F192H, P193A, P193S, W194S, W194H, W194I, V196Q, V196H, V196N, V197Q, V197H, V19′7N, L198I, L198V, L198Q, L198H, N199Q, N199S, G200Q, G200H, G200N, K201N, K201Q, V202Q, V202H, V202N, D203N, D203Q, A204Q, A204H, A204N, F205I, F205V, G207Q, G207H, G207N, G208Q, G208H, G208N, S209Q, S209H, S209N, I210Q, I210H, I210N, V211Q, V211H, V211N, E213Q, E213H, E213N, K214N, K214Q, W215S, W215H, I216Q, I216H, I216N, V217Q, V217H, V217N, T218Q, T218H, T218N, A219Q, A219H, A219N, A220Q, A220H, A220N, V223Q, V223H, V223N, E224Q, E224H, E224N, T225Q, T225H, T225N, G226Q, G226H, G226N, V227Q, V227H, V227N, K228N, K228Q, I229Q, I229H, I229N, T230Q, T230H, T230N, V231Q, V231H, V231N, V232Q, V232H, V232N, A233Q, A233H, A233N, G234Q, G234H, G234N, E235Q, E235H, E235N, I238Q, I238H, I238N, E239Q, E239H, E239N, E240Q, E240H, E240N, T241Q, T241H, T241N, E242Q, E242H, E242N, T244Q, T244H, T244N, E245Q, E245H, E245N, K247N, K247Q, R248H, R248Q, V250Q, V250H, V250N, I251Q, I251H, I251N, R252H, R252Q, I253Q, I253H, I253N, I254Q, I254H, I254N, P255A, P255S, Y259H, Y259I, A261Q, A261H, A261N, A262Q, A262H, A262N, I263Q, I263H, I263N, K265N, K265Q, Y266H, Y266I, D269N, D269Q, I270Q, I270H, I270N, A271Q, A271H, A271N, L272I, L272V, L273I, L273V, E274Q, E274H, E274N, L275I, L275V, D276N, D276Q, E277Q, E277H, E277N, P278A, P278S, L279I, L279V, V280Q, V280H, V280N, L281I, L281V, S283Q, S283H, S283N, Y284H, Y284I, V285Q, V285H, V285N, T286Q, T286H, T286N, P287A, P287S, I288Q, I288H, I288N, I290Q, I290H, I290N, A291Q, A291H, A291N, D292N, D292Q, K293N, K293Q, E294Q, E294H, E294N, Y295H, Y295I, T296Q, T296H, T296N, I298Q, I298H, I298N, F299I, F299V, L300I, L300V, K301N, K301Q, F302I, F302V, I303Q, G303H, I303N, S304Q, S304H, S304N, G305Q, G305H, I305N, Y306H, Y306I, V307Q, V307H, V307N, S308Q, S308H, S308N, G309Q, G309H, G309N, W310S, W310H, G311Q, G311H, I311N, R312H, R312Q, V313Q, V313H, V313N, F314I, F314V, K316N, K316Q, G317Q, G317H, G317N, R318H, R318Q, S319Q, S319H, S319N, A320Q, A320H, A320N, L321I, L321V, V322Q, V322H, V322N, L323I, L323V, Y325H, Y325I, L326I, L326V, R327H, R327Q, V328Q, V328H, V328N, P329A, P329S, L330I, L330V, V331Q, V331H, V331N, D332N, D332Q, R333H, R333Q, A334Q, A334H, A334N, T335Q, T335H, T335N, L337I, L337V, R338H, R338Q, S339Q, S339H, S339N, T340Q, T340H, T340N, K341N, K341Q, F342I, F342V, T343Q, T343H, T343N, I344Q, I344H, I344N, Y345H, Y345I, M348I, M348V, F349I, F349V, A351Q, A351H, A351N, G352Q, G352H, G352N, F353I, F353V, E355Q, E355H, E355N, G356Q, G356H, G356N, G357Q, G357H, G357N, R358H, R358Q, D359N, D359Q, S360Q, S360H, S360N, G363Q, G363H, G363N, D364N, D364Q, S365Q, S365H, S365N, G366Q, G366H, G366N, G367Q, G367H, G367N, P368A, P368S, V370Q, V370H, V370N, T371Q, T371H, T371N, E372Q, E372H, E372N, V373Q, V373H, V373N, E374Q, E374H, E374N, G375Q, I375H, G375N, T376Q, T376H, T376N, S377Q, S377H, S377N, F378I, F378V, L379I, L379V, T380Q, T380H, T380N, I381Q, I381H, G381N, I382Q, I382H, I382N, I383Q, I383H, I383N, S384Q, S384H, S384N, W385S, W385H, G386Q, G386H, G386N, E387Q, E387H, E387N, E388Q, E388H, E388N, A390Q, A390H, A390N, M391I, M391V, K392N, K392Q, G393Q, G393H, G393N, K394N, K394Q, Y395H, Y395I, G396Q, G396H, G396N, I397Q, I397H, I397N, Y398H, Y398I, T399Q, T399H, T399N, K400N, K400Q, V401Q, V401H, V401N, S402Q, S402H, S402N, R403H, R403Q, Y404H, Y404I, V405Q, V405H, V405N, W407S, W407H, I408Q, I408H, I408N, K409N, K409Q, E410Q, E410H, E410N, K411N, K411Q, T412Q, T412H, T412N, K413N, K413Q, L414I, L414V, T415Q, T415H, and T415N of a mature FIX polypeptide set forth in SEQ ID NO: 2 or 1035.

Provided herein are any of the above modified FIX polypeptides above that are further modified at one or more positions corresponding to amino acid positions Y1, S3, G4, K5, L6, E7, E8, F9, V10, G12, L14, E15, R16, E17, M19, E20, E21, K22, S24, F25, E26, E27, A28, R29, E30, V31, F32, E33, T35, F41, W42, K43, Y45, V46, D47, G48, D49, E52, S53, P55, L57, N58, G59, G60, K63, D64, D65, I66, Y69, W72, F75, G76, F77, E78, G79, E83, L84, V86, I90, K91, N92, G93, R94, E96, F98, K100, A103, D104, K106, V107, V108, S110, T112, E113, G114, Y115, R116, L117, A118, S123, A127, V128, P131, G133, V135, V137, S138, T140, S141, K142, L143, R145, A146, T148, V149, D152, V153, D154, Y155, V156, S158, T159, E160, A161, E162, T163, I164, L165, I168, F175, F178, T179, R180, V181, V182, G183, G184, E185, D186, A187, K188, P189, G190, F192, P193, W194, V196, V197, L198, N199, G200, K201, V202, D203, A204, F205, G207, G208, S209, I210, V211, E213, K214, W215, I216, V217, T218, A219, A220, V223, G226, V227, K228, I229, T230, V231, V232, A233, G234, E235, I238, E239, E240, E245, R248, V250, I251, R252, I253, I254, P255, Y259, A261, A262, I263, K265, Y266, D269, I270, A271, L272, L273, E274, L275, D276, E277, P278, L279, V280, L281, S283, Y284, V285, T286, P287, I288, I290, A291, D292, K293, Y295, T296, I298, F299, L300, K301, F302, G303, S304, G305, Y306, V307, S308, G309, W310, G311, R312, V313, F314, K316, G317, R318, S319, A320, L321, V322, L323, Y325, L326, R327, V328, P329, L330, V331, D332, R333, A334, T335, L337, R338, S339, T340, K341, F342, T343, I344, Y345, M348, F349, A351, G352, F353, E355, G356, G357, R358, D359, S360, G363, D364, S365, G366, G367, P368, V370, V373, E374, G375, T376, S377, F378, L379, T380, G381, I382, I383, S384, W385, G386, E387, E388, A390, M391, K392, G393, K394, Y395, G396, I397, Y398, T399, K400, V401, S402, R403, Y404, V405, W407, I408, K409, E410, K411, T412, K413, and T415 of the mature FIX polypeptide set forth in SEQ ID NO: 2 or 1035. For example, amino acid replacements at any one of the one or more further amino acid positions can include replacements of any of Y1H, Y1I, S3Q, S3H, S3N, G4Q, G4H, G4N, K5N, K5Q, L61, L6V, E7Q, E7H, E7N, E8Q, E8H, E8N, F9I, F9V, V10Q, V10H, V10N, G12Q, G12H, G12N, L141, L14V, E15Q, E15H, E15N, R16H, R16Q, E17Q, E17H, E17N, M191, M19V, E20Q, E20H, E20N, E21Q, E21H, E21N, K22N, K22Q, S24Q, S24H, S24N, F25I, F25V, E26Q, E26H, E26N, E27Q, E27H, E27N, A28Q, A28H, A28N, R29H, R29Q, E30Q, E30H, E30N, V31Q, V31H, V31N, F32I, F32V, E33Q, E33H, E33N, T35Q, T35H, T35N, T38Q, T38H, T38N, F41I, F41V, W42S, W42H, K43N, K43Q, Y45H, Y451, V46Q, V46H, V46N, D47N, D47Q, G48Q, G48H, G48N, D49N, D49Q, E52Q, E52H, E52N, S53Q, S53H, S53N, P55A, P55S, L571, L57V, N58Q, N58S, G59Q, G59H, G59N, G60Q, G60H, G60N, K63N, K63Q, D64N, D64Q, D65N, D65Q, 166Q, 166H, 166N, Y69H, Y691, W72S, W72H, F75I, F75V, G76Q, G76H, G76N, F77I, F77V, E78Q, E78H, E78N, G79Q, G79H, G79N, E83Q, E83H, E83N, L84I, L84V, V86Q, V86H, V86N, 190Q, 190H, 190N, K91N, K91Q, N92Q, N92S, G93Q, G93H, G93N, R94H, R94Q, E96Q, E96H, E96N, F981, F98V, K100N, K100Q, A103Q, A103H, A103N, D104N, D104Q, K106N, K106Q, V107Q, V107H, V107N, V108Q, V108H, V108N, S110Q, S110H, S110N, T112Q, T112H, T112N, E113Q, E113H, E113N, G114Q, G114H, G114N, Y115H, Y115I, R116H, R116Q, L117I, L117V, A118Q, A118H, A118N, S123Q, S123H, S123N, A127Q, A127H, A127N, V128Q, V128H, V128N, P131A, P131S, G133Q, G133H, G133N, V135Q, V135H, V135N, V137Q, V137H, V137N, S138Q, S138H, S138N, T140Q, T140H, T140N, S141Q, S141H, S141N, K142N, K142Q, L143I, L143V, R145H, R145Q, A146Q, A146H, A146N, T148Q, T148H, T148N, V149Q, V149H, V149N, D152N, D152Q, V153Q, V153H, V153N, D154N, D154Q, Y155H, Y155I, V156Q, V156H, V156N, S158Q, S158H, S158N, T159Q, T159H, T159N, E160Q, E160H, E160N, A161Q, A161H, A161N, E162Q, E162H, E162N, T163Q, T163H, T163N, I164Q, I164H, I164N, L165I, L165V, L165Q, L165H, I168Q, I168H, I168N, F175I, F175V, F175H, F178I, F178V, F178H, T179Q, T179H, T179N, R180H, R180Q, V181Q, V181H, V181N, V182Q, V182H, V182N, G183Q, G183H, G183N, G184Q, G184H, G184N, E185Q, E185H, E185N, D186N, D186Q, A187Q, A187H, A187N, K188N, K188Q, P189A, P189S, G190Q, G190H, G190N, F192I, F192V, F192H, P193A, P193S, W194S, W194H, W194I, V196Q, V196H, V196N, V197Q, V197H, V197N, L198I, L198V, L198Q, L198H, N199Q, N199S, G200Q, G200H, G200N, K201N, K201Q, V202Q, V202H, V202N, D203N, D203Q, A204Q, A204H, A204N, F205I, F205V, G207Q, G207H, G207N, G208Q, G208H, G208N, S209Q, S209H, S209N, I210Q, I210H, I210N, V211Q, V211H, V211N, E213Q, E213H, E213N, K214N, K214Q, W215S, W215H, I216Q, I216H, I216N, V217Q, V217H, V217N, T218Q, T218H, T218N, A219Q, A219H, A219N, A220Q, A220H, A220N, V223Q, V223H, V223N, G226Q, G226H, G226N, V227Q, V227H, V227N, K228N, K228Q, I229Q, I229H, I229N, T230Q, T230H, T230N, V231Q, V231H, V231N, V232Q, V232H, V232N, A233Q, A233H, A233N, G234Q, G234H, G234N, E235Q, E235H, E235N, I238Q, I238H, I238N, E239Q, E239H, E239N, E240Q, E240H, E240N, E245Q, E245H, E245N, R248H, R248Q, V250Q, V250H, V250N, I251Q, I251H, I251N, R252H, R252Q, I253Q, I253H, I253N, I254Q, I254H, I254N, P255A, P255S, Y259H, Y259I, A261Q, A261H, A261N, A262Q, A262H, A262N, I263Q, I263H, I263N, K265N, K265Q, Y266H, Y266I, D269N, D269Q, I270Q, I270H, I270N, A271Q, A271H, A271N, L272I, L272V, L273I, L273V, E274Q, E274H, E274N, L275I, L275V, D276N, D276Q, E277Q; E277H, E277N, P278A, P278S, L279I, L279V, V280Q, V280H, V280N, L281I, L281V, S283Q, S283H, S283N, Y284H, Y284I, V285Q, V285H, V285N, T286Q, T286H, T286N, P287A, P287S, I288Q, I288H, I288N, I290Q, I290H, I290N, A291Q, A291H, A291N, D292N, D292Q, K293N, K293Q, Y295H, Y295I, T296Q, T296H, T296N, I298Q, I298H, I298N, F299I, F299V, L300I, L300V, K301N, K301Q, F302I, F302V, G303Q, G303H, G303N, S304Q, S304H, S304N, G305Q, G305H, G305N, Y306H, Y306I, V307Q, V307H, V307N, S308Q, S308H, S308N, G309Q, G309H, G309N, W310S, W310H, G311Q, G311H, G311N, R312H, R312Q, V313Q, V313H, V313N, F314I, F314V, K316N, K316Q, G317Q, G317H, G317N, R318H, R318Q, S319Q, S319H, S319N, A320Q, A320H, A320N, L321I, L321V, V322Q, V322H, V322N, L323I, L323V, Y325H, Y325I, L326I, L326V, R327H, R327Q, V328Q, V328H, V328N, P329A, P329S, L330I, L330V, V331Q, V331H, V331N, D332N, D332Q, R333H, R333Q, A334Q, A334H, A334N, T335Q, T335H, T335N, L337I, L337V, R338H, R338Q, S339Q, S339H, S339N, T340Q, T340H, T340N, K341N, K341Q, F342I, F342V, T343Q, T343H, T343N, I344Q, I344H, I344N, Y345H, Y345I, M348I, M348V, F349I, F349V, A351Q, A351H, A351N, G352Q, G352H, G352N, F353I, F353V, E355Q, E355H, E355N, G356Q, G356H, G356N, G357Q, G357H, G357N, R358H, R358Q, D359N, D359Q, S360Q, S360H, S360N, G363Q, G363H, G363N, D364N, D364Q, S365Q, S365H, S365N, G366Q, G366H, G366N, G367Q, G367H, G367N, P368A, P368S, V370Q, V370H, V370N, V373Q, V373H, V373N, E374Q, E374H, E374N, G375Q, G375H, G375N, T376Q, T376H, T376N, S377Q, S377H, S377N, F378I, F378V, L379I, L379V, T380Q, T380H, T380N, G381Q, G381H, G381N, I382Q, I382H, I382N, I383Q, I383H, I383N, S384Q, S384H, S384N, W385S, W385H, G386Q, G386H, G386N, E387Q, E387H, E387N, E388Q, E388H, E388N, A390Q, A390H, A390N, M391I, M391V, K392N, K392Q, G393Q, G393H, G393N, K394N, K394Q, Y395H, Y395I, G396Q, G396H, G396N, I397Q, I397H, I397N, Y398H, Y398I, T399Q, T399H, T399N, K400N, K400Q, V401Q, V401H, V401N, S402Q, S402H, S402N, R403H, R403Q, Y404H, Y404I, V405Q, V405H, V405N, W407S, W407H, I408Q, I408H, I408N, K409N, K409Q, E410Q, E410H, E410N, K411N, K411Q, T412Q, T412H, T412N, K413N, K413Q, T415Q, T415H, and T415N of the mature FIX polypeptide set forth in SEQ ID NO: 2 or 1035.

Provided herein are modified FIX polypeptides containing an amino acid modification at a position corresponding to amino acid residue F 192 of a mature FIX polypeptide set forth in SEQ ID NO: 2 or 1035. Provided herein is a modified FIX polypeptide in which the amino acid modification at position F192 is a replacement of phenylalanine (F) by isoleucine (I), valine (V), or histidine (H). In a particular example, the amino acid modification at position F192 is isoleucine (I). Provided herein are modified FIX polypeptides containing an amino acid modification at F 192 that also contains a further amino acid modification at another position. For example, such a modified FIX polypeptide has 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 modifications. In one example, the further amino acid replacement is at positions corresponding to any of amino acid positions Y1, S3, G4, K5, L6, E7, E8, F9, V10, G12, L14, E15, R16, E17, M19, E20, E21, K22, S24, F25, E26, E27, A28, R29, E30, V31, F32, E33, T35, F41, W42, K43, Y45, V46, D47, G48, D49, E52, S53, P55, L57, N58, G59, G60, K63, D64, D65, I66, Y69, W72, F75, G76, F77, E78, G79, E83, L84, V86, I90, K91, N92, G93, R94, E96, F98, K100, A103, D104, K106, V107, V108, S110, T112, E113, G114, Y115, R116, L117, A118, S123, A127, V128, P131, G133, V135, V137, S138, T140, S141, K142, L143, R145, A146, T148, V149, D152, V153, D154, Y155, V156, S158, T159, E160, A161, E162, T163, I164, L165, I168, F175, F178, T179, R180, V181, V182, G183, G184, E185, D186, A187, K188, P189, G190, F192, P193, W194, V196, V197, L198, N199, G200, K201, V202, D203, A204, F205, G207, G208, S209, I210, V211, E213, K214, W215, I216, V217, T218, A219, A220, V223, G226, V227, K228, I229, T230, V231, V232, A233, G234, E235, I238, E239, E240, E245, R248, V250, I251, R252, I253, I254, P255, Y259, A261, A262, I263, K265, Y266, D269, I270, A271, L272, L273, E274, L275, D276, E277, P278, L279, V280, L281, S283, Y284, V285, T286, P287, I288, I290, A291, D292, K293, Y295, T296, I298, F299, L300, K301, F302, G303, S304, G305, Y306, V307, S308, G309, W310, G311, R312, V313, F314, K316, G317, R318, S319, A320, L321, V322, L323, Y325, L326, R327, V328, P329, L330, V331, D332, R333, A334, T335, L337, R338, S339, T340, K341, F342, T343, I344, Y345, M348, F349, A351, G352, F353, E355, G356, G357, R358, D359, S360, G363, D364, S365, G366, G367, P368, V370, V373, E374, G375, T376, S377, F378, L379, T380, G381, I382, I383, S384, W385, G386, E387, E388, A390, M391, K392, G393, K394, Y395, G396, I397, Y398, T399, K400, V401, S402, R403, Y404, V405, W407, I408, K409, E410, K411, T412, K413, and T415 of the mature FIX polypeptide set forth in SEQ ID NO: 2 or 1035. For example, amino acid replacements at any one of the further amino acid positions can include replacements of any of Y11, S3Q, S3H, S3N, G4Q, G4H, G4N, K5N, K5Q, L6I, L6V, E7Q, E7H, E7N, E8Q, E8H, E8N, F91, F9V, V10Q, V10H, V10N, G12Q, G12H, G12N, L141, L14V, E15Q, E15H, E15N, R16H, R16Q, E17Q, E17H, E17N, M191, M19V, E20Q, E20H, E20N, E21Q, E21H, E21N, K22N, K22Q, S24Q, S24H, S24N, F25I, F25V, E26Q, E26H, E26N, E27Q, E27H, E27N, A28Q, A28H, A28N, R29H, R29Q, E30Q, E30H, E30N, V31Q, V31H, V31N, F32I, F32V, E33Q, E33H, E33N, T35Q, T35H, T35N, E36Q, E36H, E36N, R37H, R37Q, T38Q, T38H, T38N, T39Q, T39H, T39N, E40Q, E40H, E40N, F41I, F41V, W42S, W42H, K43N, K43Q, Y45H, Y45I, V46Q, V46H, V46N, D47N, D47Q, G48Q, G48H, G48N, D49N, D49Q, E52Q, E52H, E52N, S53Q, S53H, S53N, P55A, P55S, L571, L57V, N58Q, N58S, G59Q, G59H, G59N, G60Q, G60H, G60N, S61Q, S61H, S61N, K63N, K63Q, D64N, D64Q, D65N, D65Q, 166Q, 166H, 166N, S68Q, S68H, S68N, Y69H, Y691, E70Q, E70H, E70N, W72S, W72H, P74A, P74S, F751, F75V, G76Q, G76H, G76N, F771, F77V, E78Q, E78H, E78N, G79Q, G79H, G79N, K80N, K80Q, E83Q, E83H, E83N, L84I, L84V, D85N, D85Q, V86Q, V86H, V86N, T87Q, T87H, T87N, 190Q, 190H, 190N, K91N, K91Q, N92Q, N92S, G93Q, G93H, G93N, R94H, R94Q, E96Q, E96H, E96N, F98I, F98V, K100N, K100Q, S102Q, S102H, S102N, A103Q, A103H, A103N, D104N, D104Q, K106N, K106Q, V107Q, V107H, V107N, V108Q, V108H, V108N, S110Q, S110H, S110N, T112Q, T112H, T112N, E113Q, E113H, E113N, G114Q, G114H, G114N, Y115H, Y115I, R116H, R116Q, L117I, L117V, A118Q, A118H, A118N, E119Q, E119H, E119N, K122N, K122Q, S123Q, S123H, S123N, E125Q, E125H, E125N, P126A, P126S, A127Q, A127H, A127N, V128Q, V128H, V128N, P129A, P129S, P131A, P131S, G133Q, G133H, G133N, R134H, R134Q, V135Q, V135H, V135N, S136Q, S136H, S136N, V137Q, V137H, V137N, S138Q, S138H, S138N, T140Q, T140H, T140N, S141Q, S141H, S141N, K142N, K142Q, L143I, L143V, T144Q, T144H, T144N, R145H, R145Q, A146Q, A146H, A146N, E147Q, E147H, E147N, T148Q, T148H, T148N, V149Q, V149H, V149N, P151A, P151S, D152N, D152Q, V153Q, V153H, V153N, D154N, D154Q, Y155H, Y155I, V156Q, V156H, V156N, S158Q, S158H, S158N, T159Q, T159H, T159N, E160Q, E160H, E160N, A161Q, A161H, A161N, E162Q, E162H, E162N, T163Q, T163H, T163N, I164Q, I164H, I164N, L165I, L165V, L165Q, L165H, D166N, D166Q, I168Q, I168H, I168N, T169Q, T169H, T169N, S171Q, S171H, S171N, T172Q, T172H, T172N, S174Q, S174H, S174N, F175I, F175V, F175H, D177N, D177Q, F178I, F178V, F178H, T179Q, T179H, T179N, R180H, R180Q, V181Q, V181H, V181N, V182Q, V182H, V182N, G183Q, G183H, G183N, G184Q, G184H, G184N, E185Q, E185H, E185N, D186N, D186Q, A187Q, A187H, A187N, K188N, K188Q, P189A, P189S, G190Q, G190H, G190N, P193A, P193S, W194S, W194H, W194I, V196Q, V196H, V196N, V197Q, V197H, V197N, L198I, L198V, L198Q, L198H, N199Q, N199S, G200Q, G200H, G200N, K201N, K201Q, V202Q, V202H, V202N, D203N, D203Q, A204Q, A204H, A204N, F205I, F205V, G207Q, G207H, G207N, G208Q, G208H, G208N, S209Q, S209H, S209N, I210Q, I210H, I210N, V211Q, V211H, V211N, E213Q, E213H, E213N, K214N, K214Q, W215S, W215H, I216Q, I216H, I216N, V217Q, V217H, V217N, T218Q, T218H, T218N, A219Q, A219H, A219N, A220Q, A220H, A220N, V223Q, V223H, V223N, E224Q, E224H, E224N, T225Q, T225H, T225N, G226Q, G226H, G226N, V227Q, V227H, V227N, K228N, K228Q, I229Q, I229H, I229N, T230Q, T230H, T230N, V231Q, V231H, V231N, V232Q, V232H, V232N, A233Q, A233H, A233N, G234Q, G234H, G234N, E235Q, E235H, E235N, I238Q, I238H, I238N, E239Q, E239H, E239N, E240Q, E240H, E240N, T241Q, T241H, T241N, E242Q, E242H, E242N, T244Q, T244H, T244N, E245Q, E245H, E245N, K247N, K247Q, R248H, R248Q, V250Q, V250H, V250N, I251Q, I251H, I251N, R252H, R252Q, I253Q, I253H, I253N, I254Q, I254H, I254N, P255A, P255S, Y259H, Y259I, A261Q, A261H, A261N, A262Q, A262H, A262N, I263Q, I263H, I263N, K265N, K265Q, Y266H, Y266I, D269N, D269Q, I270Q, I270H, I270N, A271Q, A271H, A271N, L272I, L272V, L273I, L273V, E274Q, E274H, E274N, L275I, L275V, D276N, D276Q, E277Q, E277H, E277N, P278A, P278S, L279I, L279V, V280Q, V280H, V280N, L281I, L281V, S283Q, S283H, S283N, Y284H, Y284I, V285Q, V285H, V285N, T286Q, T286H, T286N, P287A, P287S, I288Q, I288H, I288N, I290Q, I290H, I290N, A291Q, A291H, A291N, D292N, D292Q, K293N, K293Q, E294Q, E294H, E294N, Y295H, Y295I, T296Q, T296H, T296N, I298Q, I298H, I298N, F299I, F299V, L300I, L300V, K301N, K301Q, F302I, F302V, G303Q, G303H, G303N, S304Q, S304H, S304N, G305Q, G305H, G305N, Y306H, Y306I, V307Q, V307H, V307N, S308Q, S308H, S308N, G309Q, G309H, G309N, W310S, W310H, G311Q, G311H, G311N, R312H, R312Q, V313Q, V313H, V313N, F314I, F314V, K316N, K316Q, G317Q, G317H, G317N, R318H, R318Q, S319Q, S319H, S319N, A320Q, A320H, A320N, L321I, L321V, V322Q, V322H, V322N, L323I, L323V, Y325H, Y325I, L326I, L326V, R327H, R327Q, V328Q, V328H, V328N, P329A, P329S, L330I, L330V, V331Q, V331H, V331N, D332N, D332Q, R333H, R333Q, A334Q, A334H, A334N, T335Q, T335H, T335N, L337I, L337V, R338H, R338Q, S339Q, S339H, S339N, T340Q, T340H, T340N, K341N, K341Q, F342I, F342V, T343Q, T343H, T343N, I344Q, I344H, I344N, Y345H, Y345I, M348I, M348V, F349I, F349V, A351Q, A351H, A351N, G352Q, G352H, G352N, F353I, F353V, E355Q, E355H, E355N, G356Q, G356H, G356N, G357Q, G357H, G357N, R358H, R358Q, D359N, D359Q, S360Q, S360H, S360N, G363Q, G363H, G363N, D364N, D364Q, S365Q, S365H, S365N, G366Q, G366H, G366N, G367Q, G367H, G367N, P368A, P368S, V370Q, V370H, V370N, T371Q, T371H, T371N, E372Q, E372H, E372N, V373Q, V373H, V373N, E374Q, E374H, E374N, G375Q, G375H, G375N, T376Q, T376H, T376N, S377Q, S377H, S377N, F378I, F378V, L379I, L379V, T380Q, T380H, T380N, G381Q, G381H, G381N, I382Q, I382H, I382N, I383Q, I383H, I383N, S384Q, S384H, S384N, W385S, W385H, G386Q, G386H, G386N, E387Q, E387H, E387N, E388Q, E388H, E388N, A390Q, A390H, A390N, M391I, M391V, K392N, K392Q, G393Q, G393H, G393N, K394N, K394Q, Y395H, Y395I, G396Q, G396H, G396N, I397Q, I397H, I397N, Y398H, Y398I, T399Q, T399H, T399N, K400N, K400Q, V401Q, V401H, V401N, S402Q, S402H, S402N, R403H, R403Q, Y404H, Y404I, V405Q, V405H, V405N, W407S, W407H, I408Q, I408H, I408N, K409N, K409Q, E410Q, E410H, E410N, K411N, K411Q, T412Q, T412H, T412N, K413N, K413Q, L414I, L414V, T415Q, T415H, and T415N of a mature FIX polypeptide set forth in SEQ ID NO: 2 or 1035.

In some examples, exemplary amino acid modifications of a FIX polypeptide include amino acid modifications of any of T163H/F192I, I164Q/F192I, T169H/F192I, S171Q/F192I, D152N/D154N/F192I, S174Q/F192I, S174H/F192I, T179Q/F192I, T179H/F192I, T163N/I164N/F192I, D166Q/F192I, D166N/F192I, D186Q/F192I, D186N/F192I, T148A/D152N/D154N/F192I, F192I/D203Q, F192I/D203N, D152N/F192I, D152Q/F192I, T148A/D154N/F192I, D154N/F192I, D154Q/F192I, T163N/I164N, A187N/G190N, V196N/V197N, T140N/T144N, F175I/F178I, F192I/W194I, T148A/D152N, T148A/D152Q, T148A/D154N, T148A/D154Q, D152N/D154N, I168N/T169N/S171N/T172N/S174N, T179N/V181N/V182N/G183N/G184N, D152N/D154N/T148A, T163H/D166Q/F192I, T163H/D166N/F192I, T163H/D186Q/F192I, T163H/D186N/F192I, T163H/F192I/D203Q, T163H/F192I/D203N, T148A/D152N/D154N/T163H/F192I, T148A/D154N/T163H/F192I, I164Q/D166Q/F1921, I164Q/D166N/F1921, I164Q/D186Q/F192I, I164Q/D186N/F192I, I164Q/F192I/D203Q, I164Q/F192I/D203N, T148A/D152N/D154N/I164Q/F192I, T148A/D154N/I164Q/F192I, T163N/I164N/D166Q/F192I, T163N/I164N/D166N/F192I, T163N/I164N/D186Q/F192I, T163N/I164N/D186N/F192I, T163N/I164N/F192I/D203Q, T163N/I164N/F192I/D203N, T148A/D152N/D154N/T163N/I164N/F192I, T148A/D154N/T163N/I164N/F192I, D166Q/T169H/F192I, D166N/T169H/F192I, T169H/D186Q/F192I, T169H/D186N/F192I, T169H/F192I/D203Q, T169H/F192I/D203N, T148A/D152N/D154N/T169H/F192I, T148A/D154N/T169H/F192I, D166Q/S171Q/F192I, D166N/S171Q/F192I, S171Q/D186Q/F192I, S171Q/D186N/F192I, S171Q/F192I/D203Q, S171Q/F192I/D203N, T148A/D152N/D154N/S171Q/F192I, T148A/D154N/S171Q/F192I, D166Q/S174Q/F192I, D 166N/S174Q/F192I, S174Q/D186Q/F192I, S174Q/D186N/F192I, S174Q/F192I/D203Q, S174Q/F192I/D203N, T148A/D152N/D154N/S174Q/F192I, T148A/D154N/S174Q/F192I, D166Q/S174H/F192I, D166N/S174H/F192I, S174H/D186Q/F192I, S174H/D186N/F192I, S174H/F192I/D203Q, S174H/F192I/D203N, T148A/D152N/D154N/S174H/F192I, T148A/D154N/I174H/F192I, D166Q/T179Q/F192I, D166N/T179Q/F192I, T179Q/D186Q/F192I, T179Q/D186N/F192I, T179Q/F192I/D203Q, T179Q/F192I/D203N, T148A/D152N/D154N/T179Q/F192I, T148A/D154N/T179Q/F192I, D166Q/T179H/F192I, D166N/T179H/F192I, T179H/D186Q/F192I, T179H/D186N/F192I, T179H/F192I/D203Q, T179H/F192I/D203N, T148A/D152N/D154N/T179H/F192I, and T148A/D154N/T179H/F1921 of a mature FIX polypeptide set forth in SEQ ID NO: 2 or 1035. For example, a modified FIX polypeptide provided herein has a sequence of amino acids set forth in any of SEQ ID NOS: 917-1024 or 1927-2034. In particular examples, the modifications in FIX polypeptide are any of D186Q/F192I, T148A/D152N/D154N/F192I, T163H/D166Q/F192I, T163H/F192I/D203Q, T148A/D154N/T163H/F192I, I164Q/F192I/D203Q, I164Q/F192I/D203N, T148A/D154N/T163N/I164N/F192I, T169H/F192I/D203N, S174Q/F192I/D203Q, S174H/D186N/F192I, and T179Q/F192I/D203Q of a mature FIX polypeptide set forth in SEQ ID NO: 2 or 1035. In further examples, the modifications in FIX polypeptide are any of S174Q/F192I/D203Q, S174H/D186N/F192I, and T179Q/F192I/D203Q of a mature FIX polypeptide set forth in SEQ ID NO: 2 or 1035.

The modified FIX polypeptides provided herein include precursor forms and mature forms, such as modification of a wild-type human FIX polypeptide having a sequence of amino acids set forth in SEQ ID NO: 1 (precursor form) or SEQ ID NO: 2 or 1035 (mature forms). Mature forms of FIX polypeptides can include chimeric forms of FIX polypeptides such as set forth in SEQ ID NO: 1035, where homologous regions of coagulation factor family members, such as factor VII or factor X are inserted or replaced in the FIX amino acid sequence. Exemplary modified FIX polypeptides have a sequence of amino acids set forth in any of SEQ ID NOS: 3-891, 917-1034, or 1036-2044. It also is understood that amino acid modification of a FIX polypeptide can be in an allelic, species, or isoform variant of SEQ ID NO: 2 or 1035, where the allelic or species variant has 40%, 50%, 60%, 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to the polypeptide set forth in SEQ ID NO: 2 or 1035, excluding the modified positions. A modified FIX polypeptide can be a human polypeptide or a non-human polypeptide. Modified loci are identified with reference to the amino acid numbering of a known unmodified mature FIX polypeptide having a sequence of amino acids set forth in SEQ ID NO: 2 or 1035. One of skill in the art can readily determine corresponding positions on a particular polypeptide, such as by alignment of unchanged residues. Furthermore, shortened or lengthened variants with insertions or deletions of amino acids, particularly at either terminus that retain an activity readily can be prepared and the loci for corresponding mutations identified.

In one example, provided herein is a modified structural homologue of a modified FIX as described herein containing one or more amino acid replacements in the structural homologue at positions corresponding to the 3-dimensional-structurally-similar positions within the 3-D structure of the modified FIX.

Modified FIX polypeptides provided herein include FIX polypeptides modified at 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 positions as compared to an unmodified FIX polypeptide. The modified FIX polypeptides provided herein exhibit increased protein stability compared to the unmodified FIX polypeptide. Provided herein are FIX polypeptides in which increased protein stability of the modified FIX polypeptide is the result of modification to the primary sequence of the FIX polypeptide. The increased protein stability exhibited by a FIX polypeptide can be manifested as increased protease resistance. In some cases, increased protein stability of a FIX polypeptide can be due to increased resistance to proteolysis that can occur in serum, blood, saliva, digestive fluids, or in vitro when exposed to one or more proteases. The increased resistance to proteolysis is exhibited by the modified FIX when it is administered intravenously, orally, nasally, pulmonarily, or is present in the digestive tract. Such modified FIX polypeptides exhibit increased resistance to proteolysis by one or more proteases compared to the unmodified FIX. For example, the proteases can by any of pepsin, trypsin, chymotrypsin, elastase, aminopeptidase, gelatinase B, gelatinase A, α-chymotrypsin, carboxypeptidase, endoproteinase Arg-C, endoproteinase Asp-N, endoproteinase Glu-C, endoproteinase Lys-C, luminal pepsin, microvillar endopeptidase, dipeptidyl peptidase, enteropeptidase, hydrolase, NS3, factor Xa, Granzyme B, thrombin, plasmin, urokinase, tPA and PSA.

In some examples, a modified FIX polypeptide exhibits increased protein stability due to increased protease resistance to elastase. Exemplary of those modified FIX polypeptides with increased protease resistance to elastase are those with modifications corresponding to S3Q, S3H, S3N, G4Q, G4H, G4N, V10Q, V10H, V10N, G12Q, G12H, G12N, S24Q, S24H, S24N, A28Q, A28H, A28N, V31Q, V31H, V31N, T35Q, T35H, T35N, T38Q, T38H, T38N, T39Q, T39H, T39N, V46Q, V46H, V46N, G48Q, G48H, G48N, S53Q, S53H, S53N, G59Q, G59H, G59N, G60Q, G60H, G60N, S61Q, S61H, S61N, 166Q, 166H, 166N, S68Q, S68H, S68N, G76Q, G76H, G76N, G79Q, G79H, G79N, V86Q, V86H, V86N, T87Q, T87H, T87N, 190Q, 190H, 190N, G93Q, G93H, G93N, S102Q, S102H, S102N, A103Q, A103H, A103N, V107Q, V107H, V107N, V108Q, V108H, V108N, S110Q, S110H, S110N, T112Q, T112H, T112N, G114Q, G114H, G114N, A118Q, A118H, A118N, S123Q, S123H, S123N, A127Q, A127H, A127N, V128Q, V128H, V128N, G133Q, G133H, G133N, V135Q, V135H, V135N, S136Q, S136H, S136N, V137Q, V137H, V137N, S138Q, S138H, S138N, T140Q, T140H, T140N, S141Q, S141H, S141N, T144Q, T144H, T144N, A146Q, A146H, A146N, T148Q, T148H, T148N, V149Q, V149H, V149N, V153Q, V153H, V153N, V156Q, V156H, V156N, S158Q, S158H, S158N, T159Q, T159H, T159N, A161Q, A161H, A161N, T163Q, T163H, T163N, I164Q, I164H, I164N, I168Q, I168H, I168N, T169Q, T169H, T169N, S171Q, S171H, S171N, T172Q, T172H, T172N, S174Q, S174H, S174N, T179Q, T179H, T179N, V181Q, V181H, V181N, V182Q, V182H, V182N, G183Q, G183H, G183N, G184Q, G184H, G184N, A187Q, A187H, A187N, G190Q, G190H, G190N, V196Q, V196H, V196N, V197Q, V197H, V197N, G200Q, G200H, G200N, V202Q, V202H, V202N, A204Q, A204H, A204N, G207Q, G207H, G207N, G208Q, G208H, G208N, S209Q, S209H, S209N, I210Q, I210H, I210N, V211Q, V211H, V211N, I216Q, I216H, I216N, V217Q, V217H, V217N, T218Q, T218H, T218N, A219Q, A219H, A219N, A220Q, A220H, A220N, V223Q, V223H, V223N, T225Q, T225H, T225N, G226Q, G226H, G226N, V227Q, V227H, V227N, I229Q, I229H, I229N, T230Q, T230H, T230N, V231Q, V231H, V231N, V232Q, V232H, V232N, A233Q, A233H, A233N, G234Q, G234H, G234N, I238Q, I238H, I238N, T241Q, T241H, T241N, T244Q, T244H, T244N, V250Q, V250H, V250N, I251Q, I251H, I251N, I253Q, I253H, I253N, I254Q, I254H, I254N, A261Q, A261H, A261N, A262Q, A262H, A262N, I263Q, I263H, I263N, I270Q, I270H, I270N, A271Q, A271H, A271N, V280Q, V280H, V280N, S283Q, S283H, S283N, V285Q, V285H, V285N, T286Q, T286H, T286N, I288Q, I288H, I288N, I290Q, I290H, I290N, A291Q, A291H, A291N, T296Q, T296H, T296N, I298Q, I298H, I298N, G303Q, G303H, G303N, S304Q, S304H, S304N, G305Q, G305H, G305N, V307Q, V307H, V307N, S308Q, S308H, S308N, G309Q, G309H, G309N, G311Q, G311H, G311N, V313Q, V313H, V313N, G317Q, G317H, G317N, S319Q, S319H, S319N, A320Q, A320H, A320N, V322Q, V322H, V322N, V328Q, V328H, V328N, V331Q, V331H, V331N, A334Q, A334H, A334N, T335Q, T335H, T335N, S339Q, S339H, S339N, T340Q, T340H, T340N, T343Q, T343H, T343N, I344Q, I344H, I344N, A351Q, A351H, A351N, G352Q, G352H, G352N, G356Q, G356H, G356N, G357Q, G357H, G357N, S360Q, S360H, S360N, G363Q, G363H, G363N, S365Q, S365H, S365N, G366Q, G366H, G366N, G367Q, G367H, G367N, V370Q, V370H, V370N, T371Q, T371H, T371N, V373Q, V373H, V373N, G375Q, G375H, G375N, T376Q, T376H, T376N, S377Q, S377H, S377N, T380Q, T380H, T380N, G381Q, G381H, G381N, I382Q, I382H, I382N, I383Q, I383H, I383N, S384Q, S384H, S384N, G386Q, G386H, G386N, A390Q, A390H, A390N, G393Q, G393H, G393N, G396Q, G396H, G396N, I397Q, I397H, I397N, T399Q, T399H, T399N, V401Q, V401H, V401N, S402Q, S402H, S402N, V405Q, V405H, V405N, I408Q, I408H, I408N, T412Q, T412H, T412N, T415Q, T415H, and T415N of a mature FIX polypeptide set forth in SEQ ID NO: 2 or 1035.

A modified FIX polypeptide provided herein that contains one or more amino acid modifications and exhibits increased protein stability manifested as increased protease resistance to elastase also can contain any one or more further amino acid modification at amino acid positions corresponding to positions Y1, S3, G4, K5, L6, E7, E8, F9, V10, G12, L14, E15, R16, E17, M19, E20, E21, K22, S24, F25, E26, E27, A28, R29, E30, V31, F32, E33, T35, F41, W42, K43, Y45, V46, D47, G48, D49, E52, S53, P55, L57, N58, G59, G60, K63, D64, D65, I66, Y69, W72, F75, G76, F77, E78, G79, E83, L84, V86, I90, K91, N92, G93, R94, E96, F98, K100, A103, D104, K106, V107, V108, S110, T112, E113, G114, Y115, R116, L117, A118, S123, A127, V128, P131, G133, V135, V137, S138, T140, S141, K142, L143, R145, A146, T148, V149, D152, V153, D154, Y155, V156, S158, T159, E160, A161, E162, T163, I164, L165, I168, F175, F178, T179, R180, V181, V182, G183, G184, E185, D186, A187, K188, P189, G190, F192, P193, W194, V196, V197, L198, N199, G200, K201, V202, D203, A204, F205, G207, G208, S209, I210, V211, E213, K214, W215, I216, V217, T218, A219, A220, V223, G226, V227, K228, I229, T230, V231, V232, A233, G234, E235, I238, E239, E240, E245, R248, V250, I251, R252, I253, I254, P255, Y259, A261, A262, I263, K265, Y266, D269, I270, A271, L272, L273, E274, L275, D276, E277, P278, L279, V280, L281, S283, Y284, V285, T286, P287, I288, I290, A291, D292, K293, Y295, T296, I298, F299, L300, K301, F302, G303, S304, G305, Y306, V307, S308, G309, W310, G311, R312, V313, F314, K316, G317, R318, S319, A320, L321, V322, L323, Y325, L326, R327, V328, P329, L330, V331, D332, R333, A334, T335, L337, R338, S339, T340, K341, F342, T343, I344, Y345, M348, F349, A351, G352, F353, E355, G356, G357, R358, D359, S360, G363, D364, S365, G366, G367, P368, V370, V373, E374, G375, T376, S377, F378, L379, T380, G381, I382, I383, S384, W385, G386, E387, E388, A390, M391, K392, G393, K394, Y395, G396, I397, Y398, T399, K400, V401, S402, R403, Y404, V405, W407, I408, K409, E410, K411, T412, K413, and T415 of the mature FIX polypeptide set forth in SEQ ID NO: 2 or 1035. For example, amino acid replacements at any one of the further amino acid positions can include replacements of any of Y1H, Y1I, S3Q, S3H, S3N, G4Q, G4H, G4N, K5N, K5Q, L6I, L6V, E7Q, E7H, E7N, E8Q, E8H, E8N, F9I, F9V, V10Q, V10H, V10N, G12Q, G12H, G12N, L14I, L14V, E15Q, E15H, E15N, R16H, R16Q, E17Q, E17H, E17N, M191, M19V, E20Q, E20H, E20N, E21Q, E21H, E21N, K22N, K22Q, S24Q, S24H, S24N, F251, F25V, E26Q, E26H, E26N, E27Q, E27H, E27N, A28Q, A28H, A28N, R29H, R29Q, E30Q, E30H, E30N, V31Q, V31H, V31N, F321, F32V, E33Q, E33H, E33N, T35Q, T35H, T35N, T38Q, T38H, T38N, F411, F41V, W42S, W42H, K43N, K43Q, Y45H, Y45I, V46Q, V46H, V46N, D47N, D47Q, G48Q, G48H, G48N, D49N, D49Q, E52Q, E52H, E52N, S53Q, S53H, S53N, P55A, P55S, L57I, L57V, N58Q, N58S, G59Q, G59H, G59N, G60Q, G60H, G60N, K63N, K63Q, D64N, D64Q, D65N, D65Q, I66Q, I66H, I66N, Y69H, Y69I, W72S, W72H, F751, F75V, G76Q, G76H, G76N, F77I, F77V, E78Q, E78H, E78N, G79Q, G79H, G79N, E83Q, E83H, E83N, L84I, L84V, V86Q, V86H, V86N, 190Q, 190H, 190N, K91N, K91Q, N92Q, N92S, G93Q, G93H, G93N, R94H, R94Q, E96Q, E96H, E96N, F98I, F98V, K100N, K100Q, A103Q, A103H, A103N, D104N, D104Q, K106N, K106Q, V107Q, V107H, V107N, V108Q, V108H, V108N, S110Q, S110H, S110N, T112Q, T112H, T112N, E113Q, E113H, E113N, G114Q, G114H, G114N, Y115H, Y115I, R116H, R116Q, L117I, L117V, A118Q, A118H, A118N, S123Q, S123H, S123N, A127Q, A127H, A127N, V128Q, V128H, V128N, P131A, P131S, G133Q, G133H, G133N, V135Q, V135H, V135N, V137Q, V137H, V137N, S138Q, S138H, S138N, T140Q, T140H, T140N, S141Q, S141H, S141N, K142N, K142Q, L143I, L143V, R145H, R145Q, A146Q, A146H, A146N, T148Q, T148H, T148N, V149Q, V149H, V149N, D152N, D152Q, V153Q, V153H, V153N, D154N, D154Q, Y155H, Y155I, V156Q, V156H, V156N, S158Q, S158H, S158N, T159Q, T159H, T159N, E160Q, E160H, E160N, A161Q, A161H, A161N, E162Q, E162H, E162N, T163Q, T163H, T163N, I164Q, I164H, I164N, L165I, L165V, L165Q, L165H, I168Q, I168H, I168N, F175I, F175V, F175H, F178I, F178V, F178H, T179Q, T179H, T179N, R180H, R180Q, V181Q, V181H, V181N, V182Q, V182H, V182N, G183Q, G183H, G183N, G184Q, G184H, G184N, E185Q, E185H, E185N, D186N, D186Q, A187Q, A187H, A187N, K188N, K188Q, P189A, P189S, G190Q, G190H, G190N, F192I, F192V, F192H, P193A, P193S, W194S, W194H, W194I, V196Q, V196H, V196N, V197Q, V197H, V197N, L198I, L198V, L198Q, L198H, N199Q, N199S, G200Q, G200H, G200N, K201N, K201Q, V202Q, V202H, V202N, D203N, D203Q, A204Q, A204H, A204N, F205I, F205V, G207Q, G207H, G207N, G208Q, G208H, G208N, S209Q, S209H, S209N, I210Q, I210H, I210N, V211Q, V211H, V211N, E213Q, E213H, E213N, K214N, K214Q, W215S, W215H, I216Q, I216H, I216N, V217Q, V217H, V217N, T218Q, T218H, T218N, A219Q, A219H, A219N, A220Q, A220H, A220N, V223Q, V223H, V223N, G226Q, G226H, G226N, V227Q, V227H, V227N, K228N, K228Q, I229Q, I229H, I229N, T230Q, T230H, T230N, V231Q, V231H, V231N, V232Q, V232H, V232N, A233Q, A233H, A233N, G234Q, G234H, G234N, E235Q, E235H, E235N, I238Q, I238H, I238N, E239Q, E239H, E239N, E240Q, E240H, E240N, E245Q, E245H, E245N, R248H, R248Q, V250Q, V250H, V250N, I251Q, I251H, I251N, R252H, R252Q, I253Q, I253H, I253N, I254Q, I254H, I254N, P255A, P255S, Y259H, Y259I, A261Q, A261H, A261N, A262Q, A262H, A262N, I263Q, I263H, I263N, K265N, K265Q, Y266H, Y266I, D269N, D269Q, I270Q, I270H, I270N, A271Q, A271H, A271N, L272I, L272V, L273I, L273V, E274Q, E274H, E274N, L275I, L275V, D276N, D276Q, E277Q, E277H, E277N, P278A, P278S, L279I, L279V, V280Q, V280H, V280N, L281I, L281V, S283Q, S283H, S283N, Y284H, Y284I, V285Q, V285H, V285N, T286Q, T286H, T286N, P287A, P287S, I288Q, I288H, I288N, I290Q, I290H, I290N, A291Q, A291H, A291N, D292N, D292Q, K293N, K293Q, Y295H, Y295I, T296Q, T296H, T296N, I298Q, I298H, I298N, F299I, F299V, L300I, L300V, K301N, K301Q, F302I, F302V, G303Q, G303H, G303N, S304Q, S304H, S304N, G305Q, G305H, G305N, Y306H, Y306I, V307Q, V307H, V307N, S308Q, S308H, S308N, G309Q, G309H, G309N, W310S, W310H, G311Q, G311H, G311N, R312H, R312Q, V313Q, V313H, V313N, F314I, F314V, K316N, K316Q, G317Q, G317H, G317N, R318H, R318Q, S319Q, S319H, S319N, A320Q, A320H, A320N, L321I, L321V, V322Q, V322H, V322N, L323I, L323V, Y325H, Y325I, L326I, L326V, R327H, R327Q, V328Q, V328H, V328N, P329A, P329S, L330I, L330V, V331Q, V331H, V331N, D332N, D332Q, R333H, R333Q, A334Q, A334H, A334N, T335Q, T335H, T335N, L337I, L337V, R338H, R338Q, S339Q, S339H, S339N, T340Q, T340H, T340N, K341N, K341Q, F342I, F342V, T343Q, T343H, T343N, I344Q, I344H, I344N, Y345H, Y345I, M348I, M348V, F349I, F349V, A351Q, A351H, A351N, G352Q, G352H, G352N, F353I, F353V, E355Q, E355H, E355N, G356Q, G356H, G356N, G357Q, G357H, G357N, R358H, R358Q, D359N, D359Q, S360Q, S360H, S360N, G363Q, G363H, G363N, D364N, D364Q, S365Q, S365H, S365N, G366Q, G366H, G366N, G367Q, G367H, G367N, P368A, P368S, V370Q, V370H, V370N, V373Q, V373H, V373N, E374Q, E374H, E374N, G375Q, G375H, G375N, T376Q, T376H, T376N, S377Q, S377H, S377N, F378I, F378V, L379I, L379V, T380Q, T380H, T380N, G381Q, G381H, G381N, I382Q, I382H, I382N, I383Q, I383H, I383N, S384Q, S384H, S384N, W385S, W385H, G386Q, G386H, G386N, E387Q, E387H, E387N, E388Q, E388H, E388N, A390Q, A390H, A390N, M391I, M391V, K392N, K392Q, G393Q, G393H, G393N, K394N, K394Q, Y395H, Y395I, G396Q, G396H, G396N, I397Q, I397H, I397N, Y398H, Y398I, T399Q, T399H, T399N, K400N, K400Q, V401Q, V401H, V401N, S402Q, S402H, S402N, R403H, R403Q, Y404H, Y404I, V405Q, V405H, V405N, W407S, W407H, I408Q, I408H, I408N, K409N, K409Q, E410Q, E410H, E410N, K411N, K411Q, T412Q, T412H, T412N, K413N, K413Q, T415Q, T415H, and T415N of the mature FIX polypeptide set forth in SEQ ID NO: 2 or 1035.

Modified FIX polypeptides provided herein can be naked polypeptides chains or can be post-translationally modified. Exemplary post-translational modifications include glycosylation, carboxylation, hydroxylation, sulfation, phosphorylation, or conjugation to albumin or a polyethylene glycol (PEG) moiety. The modified FIX polypeptides provided herein can be further modified at one or more amino acid positions, where the modification contributes to altered immunogenicity, glycosylation, carboxylation, hydroxylation, sulfation, phosphorylation, PEGylation or protease resistance of the modified FIX polypeptide. Exemplary amino acid modifications include replacement with natural amino acids, non-natural amino acids and combinations of natural and non-natural amino acids. Such modifications can increase the stability of the FIX polypeptide.

Provided herein are any of the above modified FIX polypeptides, further containing one or more pseudo-wild type mutations. In one embodiment, the pseudo-wild-type mutations include, but are not limited to, one or more of insertions, deletions or replacements of the amino acid residue(s) of the unmodified FIX polypeptide.

Typically, the modified FIX polypeptides provided herein exhibit increased protein stability compared to the unmodified FIX polypeptide and retain one or more activities of the unmodified FIX polypeptide. Provided herein are any of the above modified FIX polypeptides exhibiting increased activity compared to the unmodified FIX. Provided herein are any of the above modified FIX polypeptides exhibiting decreased activity compared to the unmodified FIX. Activity can be assessed, for example, by measuring peptidase activity or blood coagulation in vitro or in vivo. The results of such assays correlate with an in vivo activity and hence a biological activity. In some examples the modified FIX polypeptide promotes coagulation. In other examples, the modified FIX polypeptide inhibits coagulation.

In some examples, a modified FIX polypeptide containing a modification corresponding to position F192 of a mature FIX polypeptide set forth in SEQ ID NO: 2 or 1035, and that also contains a further amino acid modification, exhibits increased protein stability and retains one or more activities of the unmodified FIX polypeptide.

Provided herein are any of the above modified FIX polypeptides, in which the increased protein stability is manifested as an increased half-life in vivo or in vitro. In one example, the increased stability is manifested as an increased half-life when administered to a subject. In another example, the modified FIX has a half-life increased by at least about or 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200%, 300%, 400%, 500%, or more compared to the half-life of unmodified FIX. In yet another example, the modified FIX also has a half-life increased by at least 1.5 times, 2 times, 3 times, 4 times, 5 times, 6 times, 7 times, 8 times, 9 times, 10 times, 20 times, 30 times, 40 times, 50 times, 60 times, 70 times, 80 times, 90 times, 100 times, 200 times, 300 times, 400 times, 500 times, 600 times, 700 times, 800 times, 900 times and 1000 times, or more times when compared to the half-life of unmodified FIX.

Provided herein are any of the above modified FIX polypeptides that is a precursor polypeptide containing a signal peptide and a propeptide. In one example, the signal sequence is amino acids 1-28 and the propeptide is amino acids 29-46 of the sequence of amino acids set forth in SEQ ID NO: 1. Provided herein are any of the above modified FIX polypeptides that do not have a signal peptide and/or propeptide. Modified FIX polypeptides without a signal peptide and propeptide are mature FIX polypeptides. In some cases, the modified FIX polypeptides provided herein are secreted. Such a secreted polypeptide has a signal sequence and propeptide sequence that is processed prior to secretion. Such secreted FIX polypeptides can contain other post-translational modifications, such as for example, glycosylation, carboxylation, hydroxylation, sulfation, and/or phosphorylation.

Provide herein are modified FIX polypeptides that include a heavy chain and a light chain of the FIX polypeptide. In some examples, a modified FIX polypeptide can include a heavy chain and lack a light chain. In some other examples, a modified FIX polypeptide can include a light chain and lack a heavy chain.

Provided herein are libraries (collections) of modified FIX polypeptides containing two, three, four, five, 10, 50, 100, 500, 1000, 10³, 10⁴ or more modified FIX polypeptides as described herein.

Provided herein are nucleic acid molecules containing a sequence of nucleotides encoding a modified FIX polypeptide as described herein. Provided herein are libraries (collections) of nucleic acid molecules comprising a plurality of the molecules as described herein.

Provided herein are vectors containing the nucleic acid molecules encoding modified FIX polypeptides as described herein. Exemplary vectors include, but are not limited to, a prokaryotic vector, a viral vector, or a eukaryotic vector. Exemplary viral vectors include adenovirus, adeno-associated-virus, retrovirus, herpes virus, lentivirus, poxvirus, and cytomegalovirus vectors. In some examples, the nucleic acid in the vector is operably linked to a promoter, such as a viral promoter or a eukaryotic promoter. Such promoters can be constitutive promoters or inducible promoters. Provided herein are libraries (collections) of such vectors containing two, three, four, five, 10, 50, 100, 500, 1000, 10³, 10⁴ or more vectors containing the nucleic acid molecules encoding modified FIX polypeptides as described herein.

Provided herein are cells containing nucleic acid molecules encoding modified FIX polypeptides as described herein. Provided herein are cells containing vectors that contain the nucleic acid molecules encoding modified FIX polypeptides as described herein. Such cells can be prokaryotic or eukaryotic cells, and can express the modified FIX polypeptides.

Provided herein are methods for expressing a modified FIX polypeptide. Such methods can include the steps of: i) introducing a nucleic acid encoding a modified FIX polypeptide or a vector containing a nucleic acid encoding a modified FIX into a cell, and ii) culturing the cell under conditions in which the encoded modified FIX is expressed. In one embodiment, cells are eukaryotic cells or prokaryotic cells. In one embodiment, the modified FIX polypeptide is post-translationally modified. In another method for expression of a modified FIX polypeptide, a nucleic acid molecule encoding a modified FIX or a vector containing a nucleic acid encoding a modified FIX is introduced into a cell-free translation system, whereby the encoded modified FIX polypeptide is expressed. In such expression methods above, the method can further include detection of the modified FIX polypeptide.

Provided herein are non-human transgenic animals containing an exogenous nucleic acid encoding a modified FIX polypeptide. Exemplary non-human transgenic animals include pigs, goats, sheep, rabbits, rats, and cows. Provided herein are methods of expressing modified FIX polypeptides in non-human transgenic animals and detecting the expressed modified FIX polypeptides. Modified FIX polypeptides can be isolated from tissues or fluids of the non-human transgenic animals, such as in serum, milk, or eggs. Such expressed modified FIX polypeptides can be post-translationally modified. For example, the modified FIX polypeptides can be glycosylated, carboxylated, hydroxylated, sulfated, phosphorylated, albuminated, or conjugated to a polyethylene glycol (PEG) moiety.

Provided herein are pharmaceutical compositions including any of the modified FIX polypeptides described herein. In some examples, the modified FIX polypeptides are any of amino acids set forth in SEQ ID NOS: 3-891, 917-1034, or 1036-2044.

In one example, the pharmaceutical compositions provided herein are formulated for local, systemic, or topical administration. For example the pharmaceutical compositions provided herein can be formulated for oral, nasal, pulmonary, buccal, transdermal, subcutaneous, intraduodenal, enteral, parenteral, intravenous, or intramuscular administration. In a particular example, the pharmaceutical compositions are formulated for oral administration.

Provided herein are pharmaceutical compositions of a modified FIX polypeptide, where the FIX polypeptide is modified by replacement of one or more amino acids in its primary structure to be resistant to a protease and the composition is formulated for oral administration.

Provided herein are pharmaceutical compositions of a modified FIX polypeptide, in which the modified FIX polypeptide comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 modifications. Provided herein are pharmaceutical compositions of a FIX polypeptide, in which only the primary sequence of the FIX polypeptide is modified, and the polypeptide exhibits increased protein stability. Such pharmaceutical compositions of a FIX polypeptide can include removal of proteolytic digestion sites.

Provided herein are pharmaceutical compositions of a modified FIX polypeptide, in which increased protein stability is manifested as increased resistance to proteolysis. In some instances, the modified FIX polypeptide in the pharmaceutical formulation exhibits increased protein stability in the gastrointestinal tract under conditions selected from exposure to saliva, exposure to proteases in the gastrointestinal tract and exposure to low pH conditions compared to an unmodified FIX polypeptide. In some instances, the increased resistance to proteolysis occurs in serum, blood, saliva, digestive fluids or in vitro when exposed to one or more proteases. Proteases include, but are not limited to one or more of a pepsin, trypsin, chymotrypsin, elastase, aminopeptidase, gelatinase B, gelatinase A, α-chymotrypsin, carboxypeptidase, endoproteinase Arg-C, endoproteinase Asp-N, endoproteinase Glu-C, endoproteinase Lys-C, luminal pepsin, microvillar endopeptidase, dipeptidyl peptidase, enteropeptidase, hydrolase, NS3, factor Xa, Granzyme B, thrombin, plasmin, urokinase, tPA and PSA. In a particular example, that protease is elastase. In some instances, the modified FIX polypeptide in the pharmaceutical formulation exhibits increased protease resistance when it is administered orally or is present in the digestive tract.

Provided herein are pharmaceutical compositions of a modified FIX polypeptide that are a FIX naked polypeptide or a post-translationally modified polypeptide, such as a FIX polypeptide that is glycosylated, carboxylated, hydroxylated, sulfated, phosphorylated albuminated, or conjugated to a polyethylene glycol (PEG) moiety.

Provided herein are pharmaceutical compositions of a modified FIX polypeptide that further comprise one or more additional amino acid modifications that contribute to altered immunogenicity, glycosylation, carboxylation, hydroxylation, sulfation, phosphorylation, PEGylation or protease resistance of the modified FIX polypeptide. Provided herein are pharmaceutical compositions of a modified FIX polypeptide, in which one or more additional amino acid modifications are selected from natural amino acids, non-natural amino acids or a combination of natural and non-natural amino acids. Provided herein are pharmaceutical compositions of a modified FIX polypeptide, in which one or more additional amino acid modifications increase stability of the FIX polypeptide.

Provided herein are pharmaceutical compositions of a modified FIX polypeptide that further comprise one or more pseudo-wild type mutations, including insertions, deletions, and replacements of the amino acid residue(s) of the unmodified FIX polypeptide.

Provided herein are pharmaceutical compositions of a modified FIX polypeptide that exhibits increased protein stability compared to the unmodified FIX polypeptide and retains one or more activities of the unmodified FIX polypeptide. Provided herein are pharmaceutical compositions of a modified FIX polypeptide that promote coagulation. Provided herein are pharmaceutical compositions of a modified FIX polypeptide that inhibit coagulation.

Provided herein are pharmaceutical compositions of a modified FIX polypeptide in which increased protein stability of the FIX polypeptide leads to increased protein half-life of the FIX polypeptide in vivo or in vitro. Increased protein stability can lead to increased protein half-life following administration to a subject. Protein half-life can be increased in an amount of at least about or 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200%, 300%, 400%, 500%, or more compared to the half-life of the unmodified FIX polypeptide. Alternatively, protein half-life can be increased in an amount of at least 6 times, at least 7 times, at least 8 times, at least 9 times, at least 10 times, at least 20 times, at least 30 times, at least 40 times, at least 50 times, at least 60 times, at least 70 times, at least 80 times, at least 90 times, at least 100 times, at least 200 times, at least 300 times, at least 400 times, at least 500 times, at least 600 times, at least 700 times, at least 800 times, at least 900 times or at least 1000 times or more compared to an unmodified protein. In one example, the modified FIX in the pharmaceutical composition exhibits increased protein half-life or bioavailability in the gastrointestinal tract.

Provided herein are pharmaceutical compositions of a modified FIX polypeptide containing a composition that also contains a pharmaceutically acceptable carrier, diluent, or excipient. Provided herein are pharmaceutical compositions of a modified FIX polypeptide, in which the excipient is a binding agent, a filler, a lubricant, a disintegrant or a wetting agent. In a particular example, the excipient is anhydrous crystalline maltose or magnesium stearate. Provided herein are pharmaceutical compositions of a modified FIX polypeptide, in which the additive is a suspending agent, an emulsifying agent, a non-aqueous vehicle, or a preservative.

Provided herein are pharmaceutical compositions of a modified FIX polypeptide, in which the pharmaceutical composition is formulated for administration in a form selected from among liquid, a pill, a tablet, a lozenge, and a capsule. In such pharmaceutical compositions, the modified FIX polypeptide is delivered to the gastrointestinal tract or the mucosa of the mouth, throat, or gastrointestinal tract. In some pharmaceutical compositions, the pill or tablet is chewable. In another example, the pill or tablet dissolves when exposed to saliva on the tongue or in the mouth. In other pharmaceutical compositions the capsule is in liquid form. Exemplary liquid pharmaceutical compositions include a solution, a syrup, or a suspension. In some pharmaceutical compositions, the tablet or capsule is enterically coated. In some pharmaceutical compositions, the modified FIX polypeptide is formulated for controlled-release.

Provided herein are pharmaceutical compositions prepared without the use of protease inhibitors, such as a Bowman-Birk inhibitor, a conjugated Bowman-Birk inhibitor, aprotinin and camostat. Provided herein are pharmaceutical compositions formulated without protective compounds.

Provided herein are pharmaceutical compositions of nucleic acid molecules encoding any of the modified FIX polypeptides described herein or a vector containing a nucleic acid molecule encoding any of the modified FIX polypeptides described herein and a pharmaceutically acceptable excipient.

Provided herein are methods of treating a subject exhibiting symptoms of or having FIX-mediated disease or condition by administering any of the pharmaceutical compositions described herein. For example, such pharmaceutical compositions can contain modified FIX polypeptides having a sequence of amino acids set forth in any one of SEQ ID NOS: 3-891, 917-1034, or 1036-2044. In some examples, the FIX-mediated disease or condition is treated by administration of an active FIX polypeptide. In other examples the FIX-mediated disease or condition is treated by administration of an inactive FIX polypeptide. Typically, treatment with the pharmaceutical composition ameliorates or alleviates the symptoms associated with the disease or condition. Provided herein are methods of monitoring the subject for changes in the symptoms associated with the FIX-mediated disease or condition.

In one example, the FIX-mediated disease or condition includes, but is not limited to hemophilia, thrombotic disease, disseminated intravascular coagulation (DIC), or hemorrhagic disease. In such an example where the disease to be treated is hemophilia, the disease or condition can be congenital or acquired. In another example where the disease to be treated is a thrombotic disease or hemorrhagic disease, the disease or condition can be, but is not limited to, ischemia, stroke, atherosclerosis, antithrombin III deficiency, or protein C deficiency. In cases where increased coagulation is desired (i.e. for hemophilia), modified FIX polypeptides that promote blood clotting are administered. In cases where decreased coagulation is desired (i.e. for thrombotic diseases), modified FIX polypeptides that inhibit blood clotting are administered.

Provided herein are methods of treating a subject exhibiting symptoms of or having a FIX-mediated disease or condition by administering modified FIX polypeptides with additional pro-coagulation factors, such as factor VIII, factor VII, vitamin K, pro-coagulants, platelet activators, vasoconstriction agents, plasminogen inhibitors, or fibrolytic inhibitors.

Provided herein are methods of treating a subject exhibiting symptoms of or having a FIX-mediated disease or condition by administering modified FIX polypeptides with additional anticoagulation factors, such as platelet inhibitors, vasodilators, fibrolytic activators, or other anticoagulants. Exemplary anticoagulants include heparin, coumarin, and hirudin. Exemplary platelet inhibitors include aspirin, naproxen, meclofenamic acid, ibuprofen, indomethacin, phenylbutazare, and ticlopidine. Exemplary fibrolytic activators include streptokinase, urokinase, and tissue plasminogen activator (t-PA).

Provided herein are articles of manufacture including, but not limited to, packaging material and a pharmaceutical composition of a modified FIX polypeptide described herein contained within the packaging material. In a particular embodiment, the pharmaceutical composition packaged within the article of manufacture is effective for treatment of a FIX-mediated disease or disorder, and the packaging material includes a label that indicates that the modified FIX is used for treatment of a FIX-mediated disease or disorder.

Provided herein are kits including a pharmaceutical composition of a modified FIX polypeptide as described herein, a device for administration of the modified FIX polypeptide and optionally instructions for administration.

Provided herein are methods for producing a modified FIX polypeptide, having an evolved predetermined property, wherein the evolved predetermined property is increased protein stability manifested as increased protease resistance. In such examples, the increased protein stability of the FIX polypeptide that is evolved is due to amino acid modifications, such that only the primary sequence of the polypeptide is modified to confer the property. In some examples, the methods include modifications of one or more additional amino acids that contribute to altered immunogenicity, glycosylation, carboxylation, hydroxylation, sulfation, phosphorylation, or PEGylation of the modified FIX polypeptide.

In one example, a method of increasing protein stability involves the step of introducing one or more amino acid modification that leads to the removal of proteolytic digestion sites such that the polypeptide exhibits increased protease resistance where the amino acid modifications are chosen from any one or more of Y1I, S3Q, S3H, S3N, G4Q, G4H, G4N, K5N, K5Q, L6I, L6V, E7Q, E7H, E7N, E8Q, E8H, E8N, F9I, F9V, V10Q, V10H, V10N, G12Q, G12H, G12N, L141, L14V, E15Q, E15H, E15N, R16H, R16Q, E17Q, E17H, E17N, M191, M19V, E20Q, E20H, E20N, E21Q, E21H, E21N, K22N, K22Q, S24Q, S24H, S24N, F25I, F25V, E26Q, E26H, E26N, E27Q, E27H, E27N, A28Q, A28H, A28N, R29H, R29Q, E30Q, E30H, E30N, V31Q, V31H, V31N, F32I, F32V, E33Q, E33H, E33N, T35Q, T35H, T35N, E36Q, E36H, E36N, R37H, R37Q, T38Q, T38H, T38N, T39Q, T39H, T39N, E40Q, E40H, E40N, F411, F41V, W42S, W42H, K43N, K43Q, Y45H, Y45I, V46Q, V46H, V46N, D47N, D47Q, G48Q, G48H, G48N, D49N, D49Q, E52Q, E52H, E52N, S53Q, S53H, S53N, P55A, P55S, L571, L57V, N58Q, N58S, G59Q, G59H, G59N, G60Q, G60H, G60N, S61Q, S61H, S61N, K63N, K63Q, D64N, D64Q, D65N, D65Q, 166Q, 166H, 166N, S68Q, S68H, S68N, Y69H, Y69I, E70Q, E70H, E70N, W72S, W72H, P74A, P74S, F75I, F75V, G76Q, G76H, G76N, F77I, F77V, E78Q, E78H, E78N, G79Q, G79H, G79N, K80N, K80Q, E83Q, E83H, E83N, L84I, L84V, D85N, D85Q, V86Q, V86H, V86N, T87Q, T87H, T87N, I90Q, I90H, 190N, K91N, K91Q, N92Q, N92S, G93Q, G93H, G93N, R94H, R94Q, E96Q, E96H, E96N, F98I, F98V, K100N, K100Q, S102Q, S102H, S102N, A103Q, A103H, A103N, D104N, D104Q, K106N, K106Q, V107Q, V107H, V10′7N, V108Q, V108H, V108N, S110Q, S110H, S110N, T112Q, T112H, T112N, E113Q, E113H, E113N, G114Q, G114H, G114N, Y115H, Y115I, R116H, R116Q, L117I, L117V, A118Q, A118H, A118N, E119Q, E119H, E119N, K122N, K122Q, S123Q, S123H, S123N, E125Q, E125H, E125N, P126A, P126S, A127Q, A127H, A127N, V128Q, V128H, V128N, P129A, P129S, P131A, P131S, G133Q, G133H, G133N, R134H, R134Q, V135Q, V135H, V135N, S136Q, S136H, S136N, V137Q, V137H, V137N, S138Q, S138H, S138N, T140Q, T140H, T140N, S141Q, S141H, S141N, K142N, K142Q, L143I, L143V, T144Q, T144H, T144N, R145H, R145Q, A146Q, A146H, A146N, E147Q, E147H, E147N, T148Q, T148H, T148N, V149Q, V149H, V149N, P151A, P151S, D152N, D152Q, V153Q, V153H, V153N, D154N, D154Q, Y155H, Y155I, V156Q, V156H, V156N, S158Q, S158H, S158N, T159Q, T159H, T159N, E160Q, E160H, E160N, A161Q, A161H, A161N, E162Q, E162H, E162N, T163Q, T163H, T163N, I164Q, I164H, I164N, L165I, L165V, L165Q, L165H, D166N, D166Q, I168Q, I168H, I168N, T169Q, T169H, T169N, S171Q, S171H, S171N, T172Q, T172H, T172N, S174Q, S174H, S174N, F175I, F175V, F175H, D177N, D177Q, F178I, F178V, F178H, T179Q, T179H, T179N, R180H, R180Q, V181Q, V181H, V181N, V182Q, V182H, V182N, G183Q, G183H, G183N, G184Q, G184H, G184N, E185Q, E185H, E185N, D186N, D186Q, A187Q, A187H, A187N, K188N, K188Q, P189A, P189S, G190Q, G190H, G190N, F192I, F192V, F192IH, P193A, P193S, W194S, W194H, W194I, V196Q, V196H, V196N, V197Q, V197H, V197N, L198I, L198V, L198Q, L198H, N199Q, N199S, G200Q, G200H, G200N, K201N, K201Q, V202Q, V202H, V202N, D203N, D203Q, A204Q, A204H, A204N, F205I, F205V, G207Q, G207H, G207N, G208Q, G208H, G208N, S209Q, S209H, S209N, I210Q, I210H, I210N, V211Q, V211H, V211N, E213Q, E213H, E213N, K214N, K214Q, W215S, W215H, I216Q, I216H, I216N, V217Q, V217H, V217N, T218Q, T218H, T218N, A219Q, A219H, A219N, A220Q, A220H, A220N, V223Q, V223H, V223N, E224Q, E224H, E224N, T225Q, T225H, T225N, G226Q, G226H, G226N, V227Q, V227H, V227N, K228N, K228Q, I229Q, I229H, I229N, T230Q, T230H, T230N, V231Q, V231H, V231N, V232Q, V232H, V232N, A233Q, A233H, A233N, G234Q, G234H, G234N, E235Q, E235H, E235N, I238Q, I238H, I238N, E239Q, E239H, E239N, E240Q, E240H, E240N, T241Q, T241H, T241N, E242Q, E242H, E242N, T244Q, T244H, T244N, E245Q, E245H, E245N, K247N, K247Q, R248H, R248Q, V250Q, V250H, V250N, I251Q, I251H, I251N, R252H, R252Q, I253Q, I253H, I253N, I254Q, I254H, I254N, P255A, P255S, Y259H, Y259I, A261Q, A261H, A261N, A262Q, A262H, A262N, I263Q, I263H, I263N, K265N, K265Q, Y266H, Y266I, D269N, D269Q, I270Q, I270H, I270N, A271Q, A271H, A271N, L272I, L272V, L273I, L273V, E274Q, E274H, E274N, L275I, L275V, D276N, D276Q, E277Q, E277H, E277N, P278A, P278S, L279I, L279V, V280Q, V280H, V280N, L281I, L281V, S283Q, S283H, S283N, Y284H, Y284I, V285Q, V285H, V285N, T286Q, T286H, T286N, P287A, P287S, I288Q, I288H, I288N, I290Q, I290H, I290N, A291Q, A291H, A291N, D292N, D292Q, K293N, K293Q, E294Q, E294H, E294N, Y295H, Y295I, T296Q, T296H, T296N, I298Q, I298H, I298N, F299I, F299V, L300I, L300V, K301N, K301Q, F302I, F302V, G303Q, G303H, G303N, S304Q, S304H, S304N, G305Q, G305H, G305N, Y306H, Y306I, V307Q, V307H, V307N, S308Q, S308H, S308N, G309Q, G309H, G309N, W310S, W310H, G311Q, G311H, G311N, R312H, R312Q, V313Q, V313H, V313N, F314I, F314V, K316N, K316Q, G317Q, G317H, G317N, R318H, R318Q, S319Q, S319H, S319N, A320Q, A320H, A320N, L321I, L321V, V322Q, V322H, V322N, L323I, L323V, Y325H, Y325I, L326I, L326V, R327H, R327Q, V328Q, V328H, V328N, P329A, P329S, L330I, L330V, V331Q, V331H, V331N, D332N, D332Q, R333H, R333Q, A334Q, A334H, A334N, T335Q, T335H, T335N, L337I, L337V, R338H, R338Q, S339Q, S339H, S339N, T340Q, T340H, T340N, K341N, K341Q, F342I, F342V, T343Q, T343H, T343N, I344Q, I344H, I344N, Y345H, Y345I, M348I, M348V, F349I, F349V, A351Q, A351H, A351N, G352Q, G352H, G352N, F353I, F353V, E355Q, E355H, E355N, G356Q, G356H, G356N, G357Q, G357H, G357N, R358H, R358Q, D359N, D359Q, S360Q, S360H, S360N, G363Q, G363H, G363N, D364N, D364Q, S365Q, S365H, S365N, G366Q, G366H, G366N, G367Q, G367H, G367N, P368A, P368S, V370Q, V370H, V370N, T371Q, T371H, T371N, E372Q, E372H, E372N, V373Q, V373H, V373N, E374Q, E374H, E374N, G375Q, G375H, G375N, T376Q, T376H, T376N, S377Q, S377H, S377N, F378I, F378V, L379I, L379V, T380Q, T380H, T380N, G381Q, G381H, G381N, I382Q, I382H, I382N, I383Q, I383H, I383N, S384Q, S384H, S384N, W385S, W385H, G386Q, G386H, G386N, E387Q, E387H, E387N, E388Q, E388H, E388N, A390Q, A390H, A390N, M391I, M391V, K392N, K392Q, G393Q, G393H, G393N, K394N, K394Q, Y395H, Y395I, G396Q, G396H, G396N, I397Q, I397H, I397N, Y398H, Y398I, T399Q, T399H, T399N, K400N, K400Q, V401Q, V401H, V401N, S402Q, S402H, S402N, R403H, R403Q, Y404H, Y404I, V405Q, V405H, V405N, W407S, W407H, I408Q, I408H, I408N, K409N, K409Q, E410Q, E410H, E410N, K411N, K411Q, T412Q, T412H, T412N, K413N, K413Q, L414I, L414V, T415Q, T415H, and T415N of a mature FIX polypeptide set forth in SEQ ID NO: 2 or 1035.

In a particular example, a method of increasing protein stability involves the step of introducing one or more amino acid modification that leads to the removal of proteolytic digestion sites recognized by elastase such that the polypeptide exhibits increased protease resistance to elastase where the amino acid modifications are chosen from any one or more of S3Q, S3H, S3N, G4Q, G4H, G4N, V10Q, V10H, V10N, G12Q, G12H, G12N, S24Q, S24H, S24N, A28Q, A28H, A28N, V31Q, V31H, V31N, T35Q, T35H, T35N, T38Q, T38H, T38N, T39Q, T39H, T39N, V46Q, V46H, V46N, G48Q, G48H, G48N, S53Q, S53H, S53N, G59Q, G59H, G59N, G60Q, G60H, G60N, S61Q, S61H, S61N, 166Q, 166H, 166N, S68Q, S68H, S68N, G76Q, G76H, G76N, G79Q, G79H, G79N, V86Q, V86H, V86N, T87Q, T87H, T87N, 190Q, 190H, 190N, G93Q, G93H, G93N, S102Q, S102H, S102N, A103Q, A103H, A103N, V107Q, V107H, V10′7N, V108Q, V108H, V108N, S110Q, S110H, S110N, T112Q, T112H, T112N, G114Q, G114H, G114N, A118Q, A118H, A118N, S123Q, S123H, S123N, A127Q, A127H, A127N, V128Q, V128H, V128N, G133Q, G133H, G133N, V135Q, V135H, V135N, S136Q, S136H, S136N, V137Q, V137H, V137N, S138Q, S138H, S138N, T140Q, T140H, T140N, S141Q, S141H, S141N, T144Q, T144H, T144N, A146Q, A146H, A146N, T148Q, T148H, T148N, V149Q, V149H, V149N, V153Q, V153H, V153N, V156Q, V156H, V156N, S158Q, S158H, S158N, T159Q, T159H, T159N, A161Q, A161H, A161N, T163Q, T163H, T163N, I164Q, I164H, I164N, I168Q, I168H, I168N, T169Q, T169H, T169N, S171Q, S171H, S171N, T172Q, T172H, T172N, S174Q, S174H, S174N, T179Q, T179H, T179N, V181Q, V181H, V181N, V182Q, V182H, V182N, G183Q, G183H, G183N, G184Q, G184H, G184N, A187Q, A187H, A187N, G190Q, G190H, G190N, V196Q, V196H, V196N, V 197Q, V197H, V197N, G200Q, G200H, G200N, V202Q, V202H, V202N, A204Q, A204H, A204N, G207Q, G207H, G207N, G208Q, G208H, G208N, S209Q, S209H, S209N, I210Q, I210H, I210N, V211Q, V211H, V211N, I216Q, I216H, I216N, V217Q, V217H, V217N, T218Q, T218H, T218N, A219Q, A219H, A219N, A220Q, A220H, A220N, V223Q, V223H, V223N, T225Q, T225H, T225N, G226Q, G226H, G226N, V227Q, V227H, V227N, I229Q, I229H, I229N, T230Q, T230H, T230N, V231Q, V231H, V231N, V232Q, V232H, V232N, A233Q, A233H, A233N, G234Q, G234H, G234N, I238Q, I238H, I238N, T241Q, T241H, T241N, T244Q, T244H, T244N, V250Q, V250H, V250N, I251Q, I251H, I251N, I253Q, I253H, I253N, I254Q, I254H, I254N, A261Q, A261H, A261N, A262Q, A262H, A262N, I263Q, I263H, I263N, I270Q, I270H, I270N, A271Q, A271H, A271N, V280Q, V280H, V280N, S283Q, S283H, S283N, V285Q, V285H, V285N, T286Q, T286H, T286N, I288Q, I288H, I288N, I290Q, I290H, I290N, A291Q, A291H, A291N, T296Q, T296H, T296N, I298Q, I298H, I298N, G303Q, G303H, G303N, S304Q, S304H, S304N, G305Q, G305H, G305N, V307Q, V307H, V307N, S308Q, S308H, S308N, G309Q, G309H, G309N, G311Q, G311H, G311N, V313Q, V313H, V313N, G317Q, G317H, G317N, S319Q, S319H, S319N, A320Q, A320H, A320N, V322Q, V322H, V322N, V328Q, V328H, V328N, V331Q, V331H, V331N, A334Q, A334H, A334N, T335Q, T335H, T335N, S339Q, S339H, S339N, T340Q, T340H, T340N, T343Q, T343H, T343N, I344Q, I344H, I344N, A351Q, A351H, A351N, G352Q, G352H, G352N, G356Q, G356H, G356N, G357Q, G357H, G357N, S360Q, S360H, S360N, G363Q, G363H, G363N, S365Q, S365H, S365N, G366Q, G366H, G366N, G367Q, G367H, G367N, V370Q, V370H, V370N, T371Q, T371H, T371N, V373Q, V373H, V373N, G375Q, G375H, G375N, T376Q, T376H, T376N, S377Q, S377H, S377N, T380Q, T380H, T380N, G381Q, G381H, G381N, I382Q, I382H, I382N, I383Q, I383H, I383N, S384Q, S384H, S384N, G386Q, G386H, G386N, A390Q, A390H, A390N, G393Q, G393H, G393N, G396Q, G396H, G396N, I397Q, I397H, I397N, T399Q, T399H, T399N, V401Q, V401H, V401N, S402Q, S402H, S402N, V405Q, V405H, V405N, I408Q, I408H, I408N, T412Q, T412H, T412N, T415Q, T415H, and T415N of a mature FIX polypeptide set forth in SEQ ID NO: 2 or 1035.

DETAILED DESCRIPTION

Outline

A. Definitions

B. Hemostasis overview

-   -   1. Clot initiation     -   2. Signal Amplification and the clotting cascade     -   3. Termination of coagulation and fibrinolysis

C. Factor IX (FIX)

-   -   1. FIX structure and function     -   2. FIX polypeptides     -   3. FIX as a biopharmaceutical

D. Exemplary methods for modifying FIX

-   -   1. Non-Restricted Rational Mutagenesis One-Dimensional         (1D)-Scanning     -   2. Two dimensional (2D) rational scanning (restricted rational         mutagenesis)         -   a. Identifying in-silico HITS         -   b. Identifying replacing amino acids         -   c. Construction of mutant proteins and biological assays     -   3. Three dimensional (3D) scanning         -   a. Homology         -   b. 3D-scanning (structural homology) methods     -   4. Super-LEADs and additive directional mutagenesis (ADM)     -   5. Multi-overlapped primer extensions

E. Modified FIX polypeptides exhibiting increased protein stability

-   -   1. Protease resistance         -   a. Serine Proteases         -   b. Matrix Metalloproteinases         -   c. Increased resistance to proteolysis by removal of             proteolytic sites         -   d. Modified FIX polypeptides exhibiting increased protease             resistance             -   i. Modified FIX polypeptides exhibiting increased                 protease resistance to elastase only         -   e. Assessment of FIX variants with increased resistance to             proteolysis     -   2. Super-LEADs     -   3. Other FIX modifications         -   a. Immunogenicity         -   b. Glycosylation         -   c. Additional modifications

F. Production of FIX polypeptides

-   -   1. Expression systems         -   a. Prokaryotic expression         -   b. Yeast         -   c. Insects and insect cells         -   d. Mammalian cells         -   e. Plants     -   2. Purification     -   3. Fusion proteins     -   4. Polypeptide modification     -   5. Nucleotide sequences

G. Assessing modified FIX polypeptide properties and activities

-   -   1. In vitro assays     -   2. Non-human animal models     -   3. Clinical Assays

H. Formulation/Packaging/Administration

-   -   1. Administration of modified FIX polypeptides         -   a. Oral administration     -   2. Administration of nucleic acids encoding modified FIX         polypeptides (gene therapy)

I. Therapeutic Uses

-   -   1. Hemophilia     -   2. Thrombotic diseases and conditions         -   a. Arterial thrombosis         -   b. Venous thrombosis and thromboembolism             -   i. Ischemic stroke     -   3. Acquired coagulation disorders         -   a. Disseminated intravascular coagulation (DIC)         -   b. Bacterial infection and periodontitis         -   c. Liver disease         -   d. Warfarin and Heparin-induced bleeding         -   e. Intracerebral hemorrhage

J. Combination Therapies

K. Articles of manufacture and kits

L. EXAMPLES

A. DEFINITIONS

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood by one of skill in the art to which the invention(s) belong. All patents, patent applications, published applications and publications, GenBank sequences, websites and other published materials referred to throughout the entire disclosure herein, unless noted otherwise, are incorporated by reference in their entirety. In the event that there is a plurality of definitions for terms herein, those in this section prevail. Where reference is made to a URL or other such identifier or address, it understood that such identifiers can change and particular information on the internet can come and go, but equivalent information can be found by searching the internet. Reference thereto evidences the availability and public dissemination of such information.

As used herein, a “factor IX” polypeptide (abbreviated herein as FIX) refers to any factor IX polypeptide, including but not limited to, a recombinantly produced polypeptide, a synthetically produced polypeptide and a factor IX polypeptide extracted or isolated from cells or tissues including, but not limited to, liver and blood. Alternative names that are used interchangeably for factor IX include Factor 9, Christmas factor, plasma thromboplastin component (PTC), coagulation factor IX, and serum factor IX. Abbreviations for factor IX include FIX and F9. Factor IX includes related polypeptides from different species including, but not limited to animals of human and non-human origin. Human factor DC (hFIX) includes factor IX, allelic variant isoforms, synthetic molecules from nucleic acids, protein isolated from human tissue and cells, and modified forms thereof. Exemplary unmodified mature human factor IX polypeptides include, but are not limited to, unmodified and wild-type native factor IX polypeptide (such as the polypeptide containing a sequence set forth in SEQ ID NO: 2) and the unmodified and wild-type precursor factor IX polypeptide that includes a propeptide and/or a signal peptide (such as, the precursor FIX polypeptide that has the sequence set forth in SEQ ID NO: 1), and a polymorphic wild-type native factor IX polypeptide that has a mutation at T148A (SEQ ID NO: 892; or its precursor containing a sequence of amino acids set forth in SEQ ID NO: 893). One of skill in the art would recognize that the referenced positions of the mature factor IX polypeptide (SEQ ID NO: 2) differ by 46 amino acid residues when compared to the precursor FIX polypeptide SEQ ID NO: 1, which is the factor IX polypeptide containing the signal peptide and propeptide sequences Thus, the first amino acid residue of SEQ ID NO: 2 “corresponds to” the forty-seventh (47^(th)) amino acid residue of SEQ ID NO: 1. The term “factor IX” also encompasses the active form of the factor IX polypeptide, also called factor IXa (FIXa), containing FIX light chain (SEQ ID NO: 894) and FIX heavy chain (SEQ ID NO: 896) linked by a disulfide bond between residues 132C and 289C. FIXa is produced from a mature FIX polypeptide (SEQ ID NO: 2) by proteolytic cleavage after amino acid residues R145 and R180. Proteolytic cleavage can be carried out, for example, by activated factor XI (FXIa) or the tissue factor/activated factor VII complex. The FIX polypeptides provided herein can be further modified, such as by chemical modification or post-translational modification. Such modifications include, but are not limited to, pegylation, albumination, glycosylation, farnysylation, carboxylation, hydroxylation, phosphorylation, and other polypeptide modifications known in the art.

Factor IX includes factor IX from any species, including human and non-human species. FIX polypeptides of non-human origin include, but are not limited to, murine, canine, feline, leporine, avian, bovine, ovine, porcine, equine, piscine, ranine, and other primate factor IX polypeptides. Exemplary FIX polypeptides of non-human origin include, for example, chimpanzee (Pan troglodytes, SEQ ID NO: 904), rhesus macaque (Macaca mulatta, SEQ ID NO: 912), mouse (Mus musculus, SEQ ID NO: 903), rat (Rattus norvegicus, SEQ ID NO: 907), Guinea pig (Cavia porcellus, SEQ ID NO: 900), pig (Sus scrofa, SEQ ID NO: 905), dog (Canis familiaris, SEQ ID NO: 899), cat (Fells catus, SEQ ID NO: 902), rabbit (Oryctolagus cuniculus, SEQ ID NO: 906), chicken (Gallus gallus, SEQ ID NO: 901), cow (Bos Taurus, SEQ ID NO: 898), sheep (Ovis aries, SEQ ID NO: 908), frog (Xenopus tropicalis, SEQ ID NO: 909), zebrafish (Danio rerio, SEQ ID NO: 910), Japanese pufferfish (Takifugu rubripes, SEQ ID NO: 911). Exemplary non-human FIX sequences that include a signal sequence and propeptide sequence include SEQ ID NOS: 899, 901-904, 909-912. Exemplary mature non-human FIX sequences that do not include a signal sequence and propeptide sequence include SEQ ID NOS: 898 and 905. Exemplary fragments of non-human FIX sequences include SEQ ID NOS: 900 and 906-908.

Human and non-human FIX polypeptides include FIX polypeptides, allelic variant isoforms, tissue-specific isoforms and allelic variants thereof, synthetic molecules prepared by translation of nucleic acids, proteins isolated from human and non-human tissue and cells, chimeric FIX polypeptides and modified forms thereof. Human and non-human FIX also include fragments or portions of FIX that are of sufficient length or include appropriate regions to retain at least one activity of the full-length mature polypeptide. Human and non-human FIX polypeptides also can include FIX polypeptides that are of sufficient length to inhibit one or more activities of a full-length mature FIX polypeptide (such as acts as an anticoagulant).

As used herein, corresponding residues refer to residues compared among or between two polypeptides that are allelic or species variants or other isoforms. One of skill in the art can readily identify residues that correspond between or among such polypeptides. For example, by aligning the sequences of factor IX polypeptides, one of skill in the art can identify corresponding residues, using conserved and identical amino acid residues as guides. For example, Y1 of SEQ ID NO: 2 (mature factor IX) corresponds to Y47 of SEQ ID NO: 1 (precursor factor IX with signal peptide and propeptide sequences). In other instances, corresponding regions can be identified. For example, the gla domain Y1 through V46 of SEQ ID NO: 2 (mature factor IX) corresponds to Y47 through V92 of SEQ ID NO: 1 (precursor factor 1× with signal peptide and propeptide sequences). One skilled in the art also can employ conserved amino acid residues as guides to find corresponding amino acid residues between and among human and non-human sequences. For example, residues R145 and R180 of SEQ ID NO: 2 (human) correspond to R191 and R226 of SEQ ID NO: 904 (chimpanzee) or R192 and R236 of SEQ ID NO: 903 (mouse).

As used herein, an “active portion or fragment of a factor IX polypeptide” refers to a portion of a human or non-human FIX polypeptide that includes at least one modification provided herein and exhibits an activity, such as one or more activities of a full-length FIX polypeptide or possesses another activity. Such activities include, but are not limited to peptidase activity, any coagulant (also referred to as procoagulant) activity, anticoagulant activity or other activity. Activity can be any percentage of activity (more or less) of the full-length polypeptide, including but not limited to, 1% of the activity, 2%, 3%, 4%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, 200%, 300%, 400%, 500%, or more activity compared to the full polypeptide. Assays to determine function or activity of modified forms of FIX include those known to those of skill in the art, and exemplary assays are included herein. Assays include, for example, activated partial thromboplastin time (aPTT). In one such assay, coagulation activity is measured as the time required for formation of a fibrin clot. Activity also includes activities possessed by a fragment or modified form that are not possessed by the full length polypeptide or unmodified polypeptide.

As used herein, “mature factor IX” refers to a FIX polypeptide that lacks a signal sequence and a propeptide sequence. Typically, a signal sequence targets a protein for secretion via the endoplasmic reticulum (ER)-golgi pathway and is cleaved following insertion into the ER during translation. A propeptide sequence typically functions in post-translational modification of the protein and is cleaved prior to secretion of the protein from the cell. Thus, a mature FIX polypeptide is typically a secreted protein. In one example, a mature human FIX polypeptide is set forth in SEQ ID NO: 2. The amino acid sequence set forth in SEQ ID NO: 2 differs from that of the precursor polypeptide set forth in SEQ ID NO: 1 in that SEQ ID NO: 2 is lacking the signal sequence, which includes residues 1-21 of SEQ ID NO: 1, and the propeptide sequence, which includes residues 29-46 of SEQ ID NO: 1.

As used herein, “native factor IX” refers to a FIX polypeptide encoded by a naturally occurring FIX gene that is present in an organism in nature, including a human or other animal. Included among native FIX polypeptides are the encoded precursor polypeptide, fragments thereof, and processed forms thereof, such as a mature form lacking the signal peptide as well as any pre- or post-translationally processed or modified form thereof. For example, humans express FIX. Exemplary native human FIX sequences are set forth in SEQ ID NOS: 1 (precursor FIX with a signal peptide and propeptide), 2 (mature FIX lacking a signal peptide), 893 (precursor FIX T148A allelic variant), or 892 (mature FIX T148A allelic variant). Also included among native FIX polypeptides are those that are post-translationally modified, including, but not limited to, modification by glycosylation, carboxylation, hydroxylation, sulfation, and phosphorylation. Native FIX polypeptides also include those that have been activated by proteolytic cleavage, typically at R145 or R180 of SEQ ID NO: 2. Other animals produce native FIX, and include, but are not limited to, chimpanzees, mice, rats, pigs, dogs, cats, rabbits, chickens, cows, sheep, frogs, and fish. Exemplary native FIX sequences from other animals are provided in SEQ ID NOS: 898-912.

As used herein, “activated Factor IX” or “FIXa” refers to a FIX polypeptide that has been proteolytically cleaved to activate the peptidase activity of the FIX polypeptide. Typically, proteolytic cleavage occurs at two sites in the mature FIX polypeptide, after R145 and R180 (SEQ ID NO: 2). Cleavage is typically carried out by activated factor XI (FXIa) in the presence of vitamin K. The cleavage products, FIX heavy chain and FIX light chain, which are held together by disulfide bonds, form the active FIX enzyme.

As used herein, a “zymogen” refers to any compound, such as a polypeptide, that is an inactive precursor of an enzyme and requires some change, such as proteolysis of the polypeptide, to become active. For example, FIX polypeptides exist in the blood plasma as zymogens until activation of the coagulation cascade, whereby the FIX polypeptides are cleaved by activated FXI.

As used herein, “unmodified target protein,” “unmodified protein,” “unmodified polypeptide,” “unmodified coagulation factor,” “unmodified FIX” and grammatical variations thereof refer to a starting polypeptide that is selected for modification as provided herein. The starting target polypeptide can be a naturally-occurring, wild-type form of a polypeptide. In addition, the starting target polypeptide can be altered or mutated, such that it differs from a native wild type isoform but is nonetheless referred to herein as a starting unmodified target protein relative to the subsequently modified polypeptides produced herein. Thus, existing proteins known in the art that have been modified to have a desired increase or decrease in a particular activity or property compared to an unmodified reference protein can be selected and used as the starting unmodified target protein. For example, a protein that has been modified from its native form by one or more single amino acid changes and possesses either an increase or decrease in a desired property, such as reduced immunogenicity (see such as, US-2004-0254106) or a change in an amino acid residue or residues to alter glycosylation, can be a target protein, referred to herein as unmodified, for further modification of either the same or a different property. Exemplary modified FIX polypeptides known in the art include any FIX polypeptide described in, for example, U.S. Pat. Nos. 6,277,618, 6,315,995, and 6,531,298 and U.S. Patent Publication Nos. 2004-0102388, 2004-0110675, 2004-0254106, 2005-0100982, and 2006-0040856.

Existing proteins known in the art that previously have been modified to have a desired alteration, such as an increase or decrease, in a particular biological activity or property compared to an unmodified or reference protein can be selected and used as provided herein for identification of structurally homologous loci on other structurally homologous target proteins. For example, a protein that has been modified by one or more single amino acid changes and possesses either an increase or decrease in a desired property or activity, such as for example resistance to proteolysis, can be utilized with the methods provided herein to identify on structurally homologous target proteins, corresponding structurally homologous loci that can be replaced with suitable replacing amino acids and tested for either an increase or decrease in the desired activity.

As used herein, an “activity” or a “functional activity” of a FIX polypeptide refers to any activity exhibited by a factor IX polypeptide. Such activities will depend on the form of the FIX polypeptide. For example, active FIX polypeptide typically exhibits coagulant or procoagulant activity, whereas a zymogen or other inactive form of a FIX polypeptide typically has anticoagulant activity. Activities of a FIX polypeptide can be tested in vitro and/or in vivo and include, but are not limited to, coagulation activity, anticoagulation activity, enzymatic activity, and peptidase activity. Activity can be assessed in vitro or in vivo using recognized assays, for example, by measuring coagulation in vitro or in vivo. The results of such assays that indicate that a polypeptide exhibits an activity can be correlated to activity of the polypeptide in vivo, in which in vivo activity can be referred to as biological activity. Activity can be any level of percentage of activity of the polypeptide, including but not limited to, 1% of the activity, 2%, 3%, 4%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, 200%, 300%, 400%, 500%, or more of activity compared to the full polypeptide. Assays to determine functionality or activity of modified forms of FIX are known to those of skill in the art. Exemplary assays to assess the functional activity of a FIX polypeptide include activated partial thromboplastin time (aPTT) assays, and are described in Example 3.

As used herein, “exhibits at least one activity” or “retains at least one activity” refers to the activity exhibited by a modified FIX polypeptide as compared to an unmodified FIX polypeptide of the same form and under the same conditions. For example, a modified FIX polypeptide that has been activated by cleavage into its heavy and light chain form is compared with an unmodified FIX polypeptide that also has been activated by cleavage into its heavy and light chain form, under the same experimental conditions, where the only difference between the two polypeptides is the modification under study. In another example, a modified FIX polypeptide in a zymogen form is compared with an unmodified FIX polypeptide in a zymogen form, under the same experimental conditions, where the only difference between the two polypeptides is the modification under study. Generally, a modified FIX polypeptide that retains an activity of an unmodified FIX polypeptide either improves or maintains the requisite biological activity (such as, coagulation activity) of an unmodified FIX polypeptide. In some instances, a modified FIX polypeptide can retain an activity that is increased compared to an unmodified FIX polypeptide. In some cases, a modified FIX polypeptide can retain an activity that is decreased compared to an unmodified FIX polypeptide. Activity of a modified FIX polypeptide can be any level of percentage of activity of the unmodified polypeptide, including but not limited to, 1% of the activity, 2%, 3%, 4%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, 200%, 300%, 400%, 500%, or more activity compared to the unmodified polypeptide. For example, a modified FIX polypeptide retains at least about or 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98% or at least 99% of the activity of the wild-type FIX polypeptide. In other embodiments, the change in activity is at least about 2 times, 3 times, 4 times, 5 times, 6 times, 7 times, 8 times, 9 times, 10 times, 20 times, 30 times, 40 times, 50 times, 60 times, 70 times, 80 times, 90 times, 100 times, 200 times, 300 times, 400 times, 500 times, 600 times, 700 times, 800 times, 900 times, 1000 times, or more times greater than unmodified FIX. Activity can be measured, for example, using assays such as those described in the Examples below.

As used herein, a “property” of a factor IX polypeptide refers to any property exhibited by a factor IX polypeptide. Such properties include, but are not limited to, protein stability, resistance to proteolysis, conformational stability, thermal tolerance, and tolerance to pH conditions. Changes in properties can alter an “activity” of the polypeptide.

As used herein, “protein stability” refers to increased protein-half-life under one or more conditions including, but not limited to, exposure to proteases, increased temperature, particular pH conditions and/or exposure to denaturing ingredients. Increased protein stability exhibited by a FIX polypeptide can be manifested as increased protease resistance, or increased conformational stability such as increased tolerance to temperature, pH, or tolerance to other denaturing ingredients. A modified polypeptide that exhibits increased protein stability in vitro or in vivo is, for example, 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200%, 300%, 400%, 500%, or more stable than an unmodified polypeptide. The protein stability of a polypeptide, for example, can be assessed in assays of protease resistance or conformational stability (i.e. resistance to temperature) to determine if an activity of the polypeptide is altered, such as is described in the Examples below. For example, the resistance of the modified FIX polypeptides compared to wild-type FIX against enzymatic cleavage by proteases (such as, α-chymotrypsin, carboxypeptidase, endoproteinase Arg-C, endoproteinase Asp-N, endoproteinase Glu-C, endoproteinase Lys-C, and trypsin) can be empirically tested by treating the polypeptides with proteases over time and then testing the polypeptides for residual functional activity such as for example, coagulation activities.

As used herein, “serum stability” refers to protein stability in serum.

As used herein, “resistance to proteolysis” refers to any amount of decreased cleavage of polypeptide by a proteolytic agent, such as a protease such that the resulting polypeptide exhibits a changed therapeutic property, such as increase half-life, increased bioavailability, particularly upon oral administration or other such properties. With respect to FIX polypeptides for which therapeutic activity requires activation, the proteases to which resistance is increased do not include required to activate the polypeptide, such as a protease that cleaves a zymogen into its active form. For example, FIX and modified FIX polypeptides provided herein when present in an inactive zymogen form require cleavage by factor XI (FXIa) or the tissue factor/activated factor VII complex to generate active Factor IX. Hence, reference to a FIX polypeptide that exhibits resistance to proteolysis or increased resistance to proteolysis refers to a polypeptide that exhibits resistance to one or more proteases, including, but not limited to, proteases of the gastrointestinal tract, digestive system, bloodstream, and serum, but retains the ability to be cleaved by factor XI (FXIa) or the tissue factor/activated factor VII complex

Resistance to proteolysis can be achieved by modifying particular amino acid residues that are susceptible to cleavage by a particular protease to render them less susceptible to cleavage compared to cleavage by the same protease under the same conditions. A modified polypeptide that exhibits increased resistance to proteolysis exhibits, for example, 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200%, 300%, 400%, 500%, or more resistance to proteolysis than an unmodified polypeptide.

As used herein, a FIX polypeptide that is resistant to proteolysis or is resistant to protease cleavage or similar terminology, is a modified FIX polypeptide that exhibits increased resistance to a protease or proteases compared to a FIX polypeptide that does not include such modification. Modifications refer to changes in the primary amino acid sequence, unless noted otherwise.

As used herein, “conformational stability” refers to any amount of increased tolerance of a polypeptide to denaturation. This can be achieved by modifying particular amino acid residues that are susceptible to denaturation conditions to render them less susceptible to denaturation under the same conditions. Conformational stability can be determined by assessing the resistance or susceptibility of a polypeptide to denaturation conditions, such as resistance to temperature or pH. A modified polypeptide that exhibits increased conformational stability exhibits, for example, 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200%, 300%, 400%, 500%, or more resistance to denaturation than an unmodified polypeptide.

As used herein, “denaturation” refers to any noncovalent change in the structure of a protein. This change can alter the secondary, tertiary and/or quaternary structure of the polypeptide molecule. Denaturation of a polypeptide can occur by, for example but not limited to, exposure to chaotropic agents such as urea and guanidine hydrochloride, detergents, temperature, pH, and reagents which cleave disulfide bridges such as dithiothreitol or dithiothreitol.

As used herein, “thermal tolerance” refers to any temperature affected or dependent change in the stability of a protein. For example, a change, such as an increased thermal tolerance, can be reflected in a decreased amount of denaturation of a polypeptide after exposure to altered (particularly increased) temperatures compared to the unmodified protein under the same conditions. A modified polypeptide that exhibits increased thermal tolerance exhibits, for example, 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200%, 300%, 400%, 500%, or more stability at varied temperatures compared to the unmodified polypeptide. For example, a modified polypeptide can exhibit increased thermal tolerance in vivo when administered to a subject compared to an unmodified polypeptide, and thereby exhibit increased serum half-life.

As used herein, “EC₅₀” refers to the effective concentration of FIX necessary to give one-half of a maximum response. For purposes herein, the response measured is any activity of a FIX polypeptide, such as but not limited to, activity in a coagulation activity assay.

As used herein, “half-life” refers to the time required for a measured parameter, such the potency, activity and effective concentration of a polypeptide molecule to fall to half of its original level, such as half of its original potency, activity, or effective concentration at time zero. Thus, the parameter, such as potency, activity, or effective concentration of a polypeptide molecule is generally measured over time. For purposes herein, half-life can be measured in vitro or in vivo. For example, the half-life of FIX or a modified FIX polypeptide can be measured in vitro by assessing its activity (i.e. coagulation activity) following incubation over increasing time under certain conditions, such as for example, after exposure to proteases, or denaturing conditions such as temperature of pH. In another example, the half-life of FIX or a modified FIX polypeptide can be measured in vivo following administration (i.e. intravenous, subcutaneous, intraduodenal, oral) of the polypeptide to a human or other animal, followed by sampling of the blood over time to determine the remaining effective concentration and/or activity of the polypeptide in the blood sample.

As used herein, formulated for oral administration refers to a formulation for ingestion into the digestive system.

As used herein, mucosal delivery refers to delivery via the mucosa and, while mucosal administration can be into the mouth, its delivery does not involve the digestive system.

As used herein, “proteases,” “proteinases” or “peptidases” are interchangeably used to refer to enzymes that catalyze the hydrolysis of covalent peptidic bonds. Proteases include, for example, serine proteases and matrix metalloproteinases. Serine protease or serine endopeptidases constitute a class of peptidases, which are characterized by the presence of a serine residue in the active center of the enzyme. Serine proteases participate in a wide range of functions in the body, including blood clotting, inflammation as well as digestive enzymes in prokaryotes and eukaryotes. The mechanism of cleavage by “serine proteases,” is based on nucleophilic attack of a targeted peptidic bond by a serine. Cysteine, threonine, or water molecules associated with aspartate or metals also can play this role. Aligned side chains of serine, histidine, and aspartate form a catalytic triad common to most serine proteases. The active site of serine proteases is shaped as a cleft where the polypeptide substrate binds. Amino acid residues are labeled from N to C termini of a polypeptide substrate (Pi, . . . , P3, P2, P1, P1′, P2′, P3′, . . . , Pj). The respective binding sub-sites are labeled (Si, . . . , S3, S2, S1, S1′, S2′, S3′, . . . , Sj). The cleavage is catalyzed between P1 and P1′.

As used herein, a matrix metalloproteinases (MMP) refers to any of a family of metal-dependent, such as Zn²⁺-dependent, endopeptidases that degrade components of the extracellular matrix (ECM). MMPs include four classes: collagenases, stromelysin, membrane-type metalloproteinases, and gelatinases. Proteolytic activities of MMPs and plasminogen activators, and their inhibitors, are important for maintaining the integrity of the ECM. Cell-ECM interactions influence and mediate a wide range of processes including proliferation, differentiation, adhesion, and migration of a variety of cell types. MMPs also process a number of cell-surface cytokines, receptors and other soluble proteins and are involved in tissue remodeling processes such as wound healing, pregnancy and angiogenesis. Under physiological conditions in vivo, MMPs are synthesized as inactive precursors (zymogens) and are cleaved to produce an active form. Additionally, the enzymes are specifically regulated by endogenous inhibitors called tissue inhibitors of matrix metalloproteinases (TIMPs).

As used herein, “factor IX-mediated disease or disorder” refers to any disease or disorder in which treatment with a factor IX (or modified factor IX) ameliorates any symptom or manifestation of the disease or disorder. Exemplary factor IX-mediated diseases and disorders include, but are not limited to, hemorrhagic disorders, such as hemophilia or thrombotic disorders, such as thromboembolism. Accordingly, a disease or condition that is treated by administration of FIX includes any disease or condition for which factor IX (or modified factor IX) is employed for treatment, including, but not limited to, hemorrhagic disorders, such as hemophilia or thrombotic disorders, such as thromboembolism.

As used herein, “procoagulant” refers to any substance that promotes blood coagulation.

As used herein, “anticoagulant” refers to any substance that inhibits blood coagulation.

As used herein, “hemophilia” refers to a bleeding disorder caused by or involving a deficiency in blood clotting factors. Hemophilia can be the result, for example, of absence, reduced expression, or reduced function of a clotting factor. The most common type of hemophilia is hemophilia A, which results from a deficiency in factor VIII. The second most common type of hemophilia is hemophilia B, which results from a deficiency in factor IX. Another, more rare form of hemophilia is hemophilia C, which results from a deficiency in factor XI.

As used herein, “congenital hemophilia” refers to types of hemophilia that are inherited. Congenital hemophilia results from mutation, deletion, insertion, or other modification of a clotting factor gene in which the production of the clotting factor is absent, reduced, or non-functional. For example, hereditary mutations in clotting factor genes, such as factor VIII and factor IX result in the congenital hemophilias, Hemophilia A and B, respectively.

As used herein, a “hereditary mutation” is a gene alteration that is passed from parent to offspring.

As used herein, “acquired hemophilia” refers to hemophilia that results from clotting factor deficiencies caused by conditions such as liver disease, vitamin K deficiency, or coumadin (warfarin) or other anti-coagulant therapy.

As used herein, “hemostasis” refers to the stopping of bleeding or blood flow in an organ or body part. The term hemostasis can encompass the entire process of blood clotting to prevent blood loss following blood vessel injury to subsequent dissolution of the blot clot following tissue repair.

As used herein fibrinolysis refers to the dissolution of a blood clot.

As used herein, thrombosis refers to the formation of a clot, or thrombus, inside a blood vessel, obstructing the flow of blood. The vessel can be any vein or artery as, for example, in a deep vein thrombosis or a coronary artery thrombosis.

As used herein, a thromboembolism is a clot that breaks loose and travels through the bloodstream.

As used herein, “thrombotic disease or condition” or “thrombolytic disease or disorder” are used interchangeably to refer to a disease characterized by the overproduction of blot clots. The clots can often break off and travel through the blood stream, causing damage to tissues, such as the lungs (pulmonary embolism), brain (ischemic stroke, transient ischemic attack), heart (heart attack/myocardial infarction, unstable angina), skin (purpura fulminans), and adrenal gland (hemorrhage). The clots also can cause deep vein thrombosis, low blood pressure (hypotension), and salt loss.

As used herein, “treating” a subject with a disease or condition means that the subject's symptoms are partially or totally alleviated, or remain static following treatment.

As used herein, treatment encompasses prophylaxis, therapy, and/or cure. Prophylaxis refers to prevention of a potential disease and/or a prevention of worsening of symptoms or progression of a disease. For example, treatment encompasses any pharmaceutical use of a modified factor IX and compositions provided herein.

As used herein, prevention refers to absolute prevention of a particular disease disorder. Since it generally is not possible to ascertain whether a disease or disorder never developed, prevention also includes reduction in the risk of developing or having a disease or disorder.

As used herein, a composition that does not include exogenously added proteases is a composition formulated without the addition of proteases, other than FIX or other active ingredient. Any additional proteases present in the composition would originate from the method of formulation.

As used herein, FIX is modified to be protease resistant by changes in primary structure. Among these are changes that do not result in changes in post-translational modification at that site.

As used herein, “therapeutically effective amount” or “therapeutically effective dose” refers to an agent, compound, material, or composition containing a compound that is at least sufficient to produce a therapeutic effect.

As used herein, “subject” to be treated includes humans and human or non-human animals. Mammals include, primates, such as humans, chimpanzees, gorillas and monkeys; domesticated animals, such as dogs, horses, cats, pigs, goats, cows, and rodents, such as mice, rats, hamsters and gerbils.

As used herein, a patient is a human subject.

As used herein, “a directed evolution method” refers to methods that “adapt” either proteins, including natural proteins, synthetic proteins or protein domains to have changed proportions, such as the ability to act in different or existing natural or artificial chemical or biological environments and/or to elicit new functions and/or to increase or decrease a given activity, and/or to modulate a given feature. Exemplary directed evolution methods include, among others, rational directed evolution methods described in U.S. Published Application Nos. US 2003-0134351 A1 and US-2004-0132977-A1.

As used herein, “two dimensional rational mutagenesis scanning (2-D scanning)” refers to the processes provided herein in which two dimensions of a particular protein sequence are scanned: (1) one dimension is to identify specific amino acid residues along the protein sequence to replace with different amino acids, referred to as is-HIT target positions, and (2) the second dimension is the amino acid type selected for replacing the particular is-HIT target, referred to as the replacing amino acid.

As used herein, “in silico” refers to research and experiments performed using a computer. In silico methods include, but are not limited to, molecular modeling studies and biomolecular docking experiments.

As used herein, “is-HIT” refers to an in silico identified amino acid position along a target protein sequence that has been identified based on i) the particular protein properties to be evolved, ii) the protein's sequence of amino acids, and/or iii) the known properties of the individual amino acids. These is-HIT loci on the protein sequence are identified without use of experimental biological methods. For example, once the protein feature(s) to be optimized is (are) selected, diverse sources of information or previous knowledge (i.e., protein primary, secondary or tertiary structures, literature, patents) are exploited to determine those amino acid positions that are amenable to improved protein fitness by replacement with a different amino acid. This step uses protein analysis “in silico.” All possible candidate amino acid positions along a target protein's primary sequence that might be involved in the feature being evolved are referred to herein as “in silico HITs” (“is-HITs”). The collection (library), of all is-HITs identified during this step represents the first dimension (target residue position) of the two-dimensional scanning methods provided herein.

As used herein, “amenable to providing the evolved predetermined property or activity” in the context of identifying is-HITs refers to an amino acid position on a protein that is contemplated, based on in silico analysis, to possess properties or features that when replaced result in the desired activity being evolved. The phrase “amenable to providing the evolved predetermined property or activity” in the context of identifying replacement amino acids refers to a particular amino acid type that is contemplated, based on in silico analysis, to possess properties or features that when used to replace the original amino acid in the unmodified starting protein result in the evolution of a desired or preselected activity.

As used herein, “high-throughput screening” (HTS) refers to processes that test a large number of samples, such as samples of test proteins or cells containing nucleic acids encoding the proteins of interest to identify structures of interest or to identify test compounds that interact with the variant proteins or cells containing them. HTS operations are amenable to automation and are typically computerized to handle sample preparation, assay procedures, and the subsequent processing of large volumes of data.

As used herein, the term “restricted,” in the context of the identification of is-HIT amino acid positions along the amino acid residues in a protein selected for amino acid replacement and/or the identification of replacing amino acids, means that fewer than all amino acids on the protein-backbone are selected for amino acid replacement and/or fewer than all of the remaining 19 amino acids available to replace the original amino acid present in the unmodified starting protein are selected for replacement. In particular embodiments of the methods provided herein, the is-HIT amino acid positions are restricted such that fewer than all amino acids on the protein-backbone are selected for amino acid replacement. In other embodiments, the replacing amino acids are restricted such that fewer than all of the remaining 19 amino acids available to replace the native amino acid present in the unmodified starting protein are selected as replacing amino acids. In an exemplary embodiment, both of the scans to identify is-HIT amino acid positions and the replacing amino acids are restricted such that fewer than all amino acids on the protein-backbone are selected for amino acid replacement and fewer than all of the remaining 19 amino acids available to replace the native amino acid are selected for replacement.

As used herein, “candidate LEADs” are mutant proteins that are designed to have an alteration in property, activity or other attribute, typically a predetermined or preselected property, activity or other attribute, such as a, chemical, physical or biological property or activity in which such alteration is sought. The alteration can add, alter, remove or otherwise change a property, activity or other attribute of a polypeptide. In the methods herein, candidate LEADs are generally generated by systematically replacing is-HITS loci in a protein or a domain thereof with typically a restricted subset, or all, of the remaining 19 amino acids, such as obtained using PAM analysis. Candidate LEADs can be generated by other methods known to those of skill in the art tested by the high throughput methods herein.

As used herein, “LEADs” are “candidate LEADs” whose property, activity or other attribute has been changed, optimized, improved, added or eliminated. For purposes herein a “LEAD” typically has activity with respect to a property or activity of interest in an unmodified polypeptide that exhibits such activity or property that differs by at least about or 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200%, 300%, 400%, 500%, or more from the unmodified and/or wild type (native) protein. In certain embodiments, the change in activity is at least about 2 times, 3 times, 4 times, 5 times, 6 times, 7 times, 8 times, 9 times, 10 times, 20 times, 30 times, 40 times, 50 times, 60 times, 70 times, 80 times, 90 times, 100 times, 200 times, 300 times, 400 times, 500 times, 600 times, 700 times, 800 times, 900 times, 1000 times, or more times greater than the activity of the unmodified and/or wild type (native) protein. The desired alteration, which can be either an increase or a reduction in activity, depends upon the function or property of interest (such as, at least about or 10%, at least about or 20%, etc.). The LEADs can be further optimized by replacement of a plurality (2 or more) of “is-HIT” target positions on the same protein molecule to generate “super-LEADs.”

As used herein, the term “super-LEAD” refers to protein mutants (variants) obtained by adding the single mutations present in two or more of the LEAD molecules in a single protein molecule. Accordingly, in the context of the modified proteins provided herein, the phrase “proteins comprising one or more single amino acid replacements” encompasses addition of two or more of the mutations described herein for one respective protein. For example, the modified proteins provided herein containing one or more single amino acid replacements can have any of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more of the amino acid replacements at the disclosed replacement positions. The collection of super-LEAD mutant molecules is generated, tested, and phenotypically characterized one-by-one in addressable arrays. Super-LEAD mutant molecules are molecules containing a variable number and type of LEAD mutation. Those molecules displaying further improved fitness for the particular feature being evolved, are referred to as super-LEADs. Super-LEADs can be generated by other methods known to those of skill in the art and tested by the high throughput methods herein. For purposes herein, a super-LEAD typically has activity with respect to the function of interest that differs from the altered activity (or the new activity or eliminated activity) of a LEAD by a desired amount, such as at least about or 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200%, 300%, 400%, 500%, or more from the LEAD mutant from which it is derived. As with LEADs, the change in the activity for super-LEADs is dependent upon the activity that is being “evolved.” The desired alteration, which can be either an increase or a reduction in activity, depends upon the function or property of interest. The desired alteration also can be an addition or elimination of a property or activity.

As used herein, the phrase “altered loci” refers to the is-HIT amino acid positions in the LEADs or super-LEADs that are replaced with different replacing amino acids resulting in the desired altered phenotype or activity.

As used herein, an “exposed residue” presents more than 15% of its surface exposed to the solvent.

As used herein, the phrase “structural homology” refers to the degree of coincidence in space between two or more protein backbones. Protein backbones that adopt the same protein structure, fold and show similarity upon three-dimensional structural superposition in space can be considered structurally homologous. Structural homology is not based on sequence homology, but rather on three-dimensional homology. Two amino acids in two different proteins said to be homologous based on structural homology between those proteins do not necessarily need to be in sequence-based homologous regions. For example, protein backbones that have a root mean squared (RMS) deviation of less than 3.5, 3.0, 2.5, 2.0, 1.7 or 1.5 angstroms at a given space position or defined region between each other can be considered to be structurally homologous in that region and are referred to herein as having a “high coincidence” between their backbones. It is contemplated herein that substantially equivalent (such as, “structurally related”) amino acid positions that are located on two or more different protein sequences that share a certain degree of structural homology have comparable functional tasks; also referred to herein as “structurally homologous loci.” These two amino acids then can be said to be “structurally similar” or “structurally related” with each other, even if their precise primary linear positions on the sequences of amino acids, when these sequences are aligned, do not match with each other. Amino acids that are “structurally related” can be far away from each other in the primary protein sequences, when these sequences are aligned following the rules of classical sequence homology.

As used herein, a “structural homolog” is a protein that is generated by structural homology. Exemplary FIX structural homologs include many other vitamin K dependent plasma proteins, including, for example, prothrombin, factor VII, factor X, and protein C.

As used herein, “variant,” “factor IX variant,” “modified factor IX polypeptides” and “modified factor IX proteins” refers to a FIX polypeptide that has one or more mutations compared to an unmodified factor IX polypeptide. The one or more mutations can be one or amino acid replacements, insertions or deletions and any combination thereof. Typically, a modified FIX polypeptide has one or more modifications in its primary sequence compared to an unmodified FIX polypeptide. For example, a modified FIX polypeptide provided herein can have 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more mutations compared to an unmodified FIX polypeptide. Modifications that confer a property (such as, increased protein stability or increased protease resistance) by virtue of a change in a primary amino acid sequence do not require a change in post-translational modification of the modified polypeptide to confer the property. Any length polypeptide is contemplated as long as the resulting polypeptide exhibits at least one FIX activity associated with a native FIX polypeptide or inhibits an activity at least one FIX activity associated with a native FIX polypeptide (such as acts as an anticoagulant).

As used herein, a “single amino acid replacement” refers to the replacement of one amino acid by another amino acid. The replacement can be by a natural amino acid or non-natural amino acids. When one amino acid is replaced by another amino acid in a protein, the total number of amino acids in the protein is unchanged.

As used herein, the phrase “only one amino acid replacement occurs on each target protein” refers to the modification of a target protein, such that it differs from the unmodified form of the target protein by a single amino acid change. For example, in one embodiment, mutagenesis is performed by the replacement of a single amino acid residue at only one is-HIT target position on the protein backbone (such as, “one-by-one” in addressable arrays), such that each individual mutant generated is the single product of each single mutagenesis reaction. The single amino acid replacement mutagenesis reactions are repeated for each of the replacing amino acids selected at each of the is-HIT target positions. Thus, a plurality of mutant protein molecules are produced, whereby each mutant protein contains a single amino acid replacement at only one of the is-HIT target positions.

As used herein, the phrase “pseudo-wild type,” in the context of single or multiple amino acid replacements, are those amino acids that, while different from the original (such as, such as native) amino acid at a given amino acid position, can replace the native one at that position without introducing any measurable change in a particular protein activity. A population (library) of sets of nucleic acid molecules encoding a collection of mutant molecules is generated and phenotypically characterized such that proteins with sequences of amino acids different from the original amino acid, but that still elicit substantially the same level (i.e., at least about or 10%, 50%, 80%, 90%, 95%, 100%, depending upon the protein) and type of desired activity as the original protein are selected. A library, contains three, four, five, 10, 50, 100, 500, 1000, 10³, 10⁴ or more modified FIX polypeptides.

As used herein, “in a position or positions corresponding to an amino acid position” of a protein, refers to amino acid positions that are determined to correspond to one another based on sequence and/or structural alignments with a specified reference protein. For example, in a position corresponding to an amino acid position of human FIX set forth as SEQ ID NO: 2 can be determined empirically by aligning the sequence of amino acids set forth in SEQ ID NO: 2 with a particular FIX polypeptide of interest. Corresponding positions can be determined by such alignment by one of skill in the art using manual alignments or by using the numerous alignment programs available (for example, BLASTP). Corresponding positions also can be based on structural alignments, for example by using computer simulated alignments of protein structure. Recitation that amino acids of a polypeptide correspond to amino acids in a disclosed sequence refers to amino acids identified upon alignment of the polypeptide with the disclosed sequence to maximize identity or homology (where conserved amino acids are aligned) using a standard alignment algorithm, such as the GAP algorithm.

As used herein, “at a position corresponding to” refers to a position of interest (i.e., base number or residue number) in a nucleic acid molecule or protein relative to the position in another reference nucleic acid molecule or protein. The position of interest to the position in another reference protein can be in, for example, a precursor protein, an allelic variant, a heterologous protein, an amino acid sequence from the same protein of another species, etc. Corresponding positions can be determined by comparing and aligning sequences to maximize the number of matching nucleotides or residues, for example, such that identity between the sequences is greater than 95%, 96%, 97%, 98% or 99% or more. The position of interest is then given the number assigned in the reference nucleic acid molecule.

As used herein, the terms “homology” and “identity”” are used interchangeably, but homology for proteins can include conservative amino acid changes. In general to identify corresponding positions the sequences of amino acids are aligned so that the highest order match is obtained (see, such as: Computational Molecular Biology, Lesk, A. M., ed., Oxford University Press, New York, 1988; Biocomputing: Informatics and Genome Projects, Smith, D. W., ed., Academic Press, New York, 1993; Computer Analysis of Sequence Data, Part I, Griffin, A. M., and Griffin, H. G., eds., Humana Press, New Jersey, 1994; Sequence Analysis in Molecular Biology, von Heinje, G., Academic Press, 1987; and Sequence Analysis Primer, Gribskov, M. and Devereux, J., eds., M Stockton Press, New York, 1991; Carillo et al. (1988) SIAM J Applied Math 48:1073).

As use herein, “sequence identity” refers to the number of identical amino acids (or nucleotide bases) in a comparison between a test and a reference polypeptide or polynucleotide. Homologous polypeptides refer to a pre-determined number of identical or homologous amino acid residues. Homology includes conservative amino acid substitutions as well identical residues. Sequence identity can be determined by standard alignment algorithm programs used with default gap penalties established by each supplier. Homologous nucleic acid molecules refer to a pre-determined number of identical or homologous nucleotides. Homology includes substitutions that do not change the encoded amino acid (i.e., “silent substitutions”) as well identical residues. Substantially homologous nucleic acid molecules hybridize typically at moderate stringency or at high stringency all along the length of the nucleic acid or along at least about 70%, 80%, or 90% of the full-length nucleic acid molecule of interest. Also contemplated are nucleic acid molecules that contain degenerate codons in place of codons in the hybridizing nucleic acid molecule. (For determination of homology of proteins, conservative amino acids can be aligned as well as identical amino acids; in this case, percentage of identity and percentage homology vary). Whether any two nucleic acid molecules have nucleotide sequences (or any two polypeptides have amino acid sequences) that are at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% “identical” can be determined using known computer algorithms such as the “FASTA” program, using for example, the default parameters as in Pearson et al. (1988) Proc. Natl. Acad. Sci. USA 85: 2444 (other programs include the GCG program package (Devereux, J., et al. (1984) Nucleic Acids Research 12(I): 387), BLASTP, BLASTN, FASTA (Atschul, S. F., et al. (1990) J. Molec. Biol. 215:403; Guide to Huge Computers, Martin J. Bishop, ed., Academic Press, San Diego (1994), and Carillo et al. (1988) SIAM J Applied Math 48: 1073). For example, the BLAST function of the National Center for Biotechnology Information database can be used to determine identity. Other commercially or publicly available programs include, DNAStar “MegAlign” program (Madison, Wis.) and the University of Wisconsin Genetics Computer Group (UWG) “Gap” program (Madison Wis.). Percent homology or identity of proteins and/or nucleic acid molecules can be determined, for example, by comparing sequence information using a GAP computer program (such as, Needleman et al. (1970) J. Mol. Biol. 48: 443, as revised by Smith and Waterman (1981) Adv. Appl. Math. 2: 482. Briefly, a GAP program defines similarity as the number of aligned symbols (i.e., nucleotides or amino acids) which are similar, divided by the total number of symbols in the shorter of the two sequences. Default parameters for the GAP program can include: (1) a unary comparison matrix (containing a value of 1 for identities and 0 for non identities) and the weighted comparison matrix of Gribskov et al. (1986) Nucl. Acids Res. 14: 6745, as described by Schwartz and Dayhoff, eds. (1979) Atlas of Protein Sequence and Structure, National Biomedical Research Foundation, pp. 353-358; (2) a penalty of 3.0 for each gap and an additional 0.10 penalty for each symbol in each gap; and (3) no penalty for end gaps.

Therefore, as used herein, the term “identity” represents a comparison between a test and a reference polypeptide or polynucleotide. In one non-limiting example, “at least 90% identical to” refers to percent identities from 90 to 100% relative to the reference polypeptides. Identity at a level of 90% or more is indicative of the fact that, assuming for exemplification purposes a test and reference polynucleotide length of 100 amino acids are compared, no more than 10% (i.e., 10 out of 100) of amino acids in the test polypeptide differs from that of the reference polypeptides. Similar comparisons can be made between a test and reference polynucleotides. Such differences can be represented as point mutations randomly distributed over the entire length of an amino acid sequence or they can be clustered in one or more locations of varying length up to the maximum allowable, such as, 10/100 amino acid difference (approximately 90% identity). Differences are defined as nucleic acid or amino acid substitutions, insertions or deletions. At the level of homologies or identities above about 85-90%, the result should be independent of the program and gap parameters set; such high levels of identity can be assessed readily, often without relying on software.

As used herein, “corresponding structurally-related” positions on two or more polypeptides, such as FIX polypeptides and other coagulation factors, refer to those amino acid positions determined based upon structural homology to maximize tri-dimensional overlapping between or among polypeptides.

As used herein, the phrase “sequence-related proteins” refers to proteins that have at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 95% amino acid sequence identity or homology with each other.

As used herein, families of non-related proteins or “sequence-non-related proteins” refer to proteins having less than 50%, less than 40%, less than 30%, less than 20% amino acid identity, or homology with each other.

As used herein, it also is understood that the terms “substantially identical” or “similar” varies with the context as understood by those skilled in the relevant art.

As used herein, “a naked polypeptide chain” refers to a polypeptide that is not post-translationally modified or otherwise chemically modified, but contains only covalently linked amino acids.

As used herein, a polypeptide complex includes polypeptides produced by chemical modification or post-translational modification. Such modifications include, but are not limited to, pegylation, albumination, glycosylation, farnysylation, carboxylation, hydroxylation, phosphorylation, and other polypeptide modifications known in the art.

As used herein, “output signal” refers to parameters that can be followed over time and, optionally, quantified. For example, when a recombinant protein is introduced into a cell, the cell containing the recombinant protein undergoes a number of changes. Any such change that can be monitored and used to assess the transformation or transfection is an output signal, and the cell is referred to as a reporter cell; the encoding nucleic acid is referred to as a reporter gene; and the construct that includes the encoding nucleic acid is a reporter construct. Output signals include, but are not limited to, enzyme activity, fluorescence, luminescence, amount of product produced, and other such signals. Output signals include expression of a gene or gene product, including heterologous genes (transgenes) inserted into the plasmid virus. Output signals are a function of time (“t”) and are related to the amount of protein used in the composition. For higher concentrations of protein, the output signal can be higher or lower. For any particular concentration, the output signal increases as a function of time until a plateau is reached. Output signals also can measure the interaction between cells, expressing heterologous genes and biological agents.

As used herein, a population of sets of nucleic acid molecules encoding a collection (library) of mutants refers to a collection of plasmids or other vehicles that carry (encode) the gene variants. Thus, individual plasmids or other individual vehicles carry individual gene variants. Each element (member) of the collection is physically separated from the others in an appropriate addressable array and has been generated as the single product of an independent mutagenesis reaction. When a collection (library) of such proteins is contemplated, it will be so-stated. A library contains three, four, five, 10, 50, 100, 500, 1000, 10³, 10⁴ or more modified FIX polypeptides.

As used herein, a “reporter cell” is the cell that undergoes the change in response to a condition. For example, in response to exposure to a protein or a virus or to a change in its external or internal environment, the reporter cell “reports” (i.e., displays or exhibits the change).

As used herein, “reporter” or “reporter moiety” refers to any moiety that allows for the detection of a molecule of interest, such as a protein expressed by a cell. Reporter moieties include, but are not limited to, fluorescent proteins (such as, red, blue, and green fluorescent proteins), LacZ and other detectable proteins and gene products. For expression in cells, nucleic acids encoding the reporter moiety can be expressed as a fusion protein with a protein of interest or under the control of a promoter of interest.

As used herein, phenotype refers to the physical, physiological, or other manifestation of a genotype (a sequence of a gene). In methods herein, phenotypes that result from alteration of a genotype are assessed.

As used herein, culture medium is any medium suitable for supporting the viability, growth, and/or differentiation of mammalian cells ex vivo. Any such medium is known to those of skill in the art. Examples of culture medium include, but are not limited to, X-Vivo15 (BioWhittaker), RPMI 1640, DMEM, Ham=s F12, McCoys 5A and Medium 199. The medium can be supplemented with additional ingredients including serum, serum proteins, growth suppressing, and growth promoting substances, such as mitogenic monoclonal antibodies and selective agents for selecting genetically engineered or modified cells.

As used herein, the amino acids that occur in the various sequences of amino acids provided herein are identified according to their known, three-letter or one-letter abbreviations (Table 1). The nucleotides which occur in the various nucleic acid fragments are designated with the standard single-letter designations used routinely in the art.

As used herein, an “amino acid” is an organic compound containing an amino group and a carboxylic acid group. A polypeptide comprises two or more amino acids. For purposes herein, amino acids include the twenty naturally-occurring amino acids, non-natural amino acids, and amino acid analogs (i.e., amino acids wherein the α-carbon has a side chain).

As used herein, the abbreviations for any protective groups, amino acids and other compounds are, unless indicated otherwise, in accord with their common usage, recognized abbreviations, or the IUPAC-IUB Commission on Biochemical Nomenclature (1972) Biochem. 11: 1726). Each naturally occurring L-amino acid is identified by the standard three letter code (or single letter code) or the standard three letter code (or single letter code) with the prefix “L-;” the prefix “D-” indicates that the stereoisomeric form of the amino acid is D.

As used herein, “amino acid residue” refers to an amino acid formed upon chemical digestion (hydrolysis) of a polypeptide at its peptide linkages. The amino acid residues described herein are presumed to be in the “L” isomeric form. Residues in the “D” isomeric form, which are so designated, can be substituted for any L-amino acid residue as long as the desired functional property is retained by the polypeptide. “NH₂” refers to the free amino group present at the amino terminus of a polypeptide. “COOH” refers to the free carboxy group present at the carboxyl terminus of a polypeptide. In keeping with standard polypeptide nomenclature described in (1969) J. Biol. Chem., 243: 3552-3559, and adopted 37 C.F.R. □§§1.821-1.822, abbreviations for amino acid residues are shown in Table 1:

TABLE 1 Table of Correspondence SYMBOL 1-Letter 3-Letter AMINO ACID Y Tyr tyrosine G Gly glycine F Phe phenylalanine M Met methionine A Ala alanine S Ser serine I Ile isoleucine L Leu leucine T Thr threonine V Val valine P Pro proline K Lys lysine H His histidine Q Gln glutamine E Glu glutamic acid Z Glx Glu and/or Gln W Trp tryptophan R Arg arginine D Asp aspartic acid N Asn asparagine B Asx Asn and/or Asp C Cys cysteine X Xaa Unknown or other

All amino acid residue sequences represented herein by formulae have a left to right orientation in the conventional direction of amino-terminus to carboxyl-terminus. In addition, the phrase “amino acid residue” is broadly defined to include the amino acids listed in the Table of Correspondence (Table 1) and modified and unusual amino acids, such as those referred to in 37 C.F.R. §§1.821-1.822, and incorporated herein by reference. Furthermore, a dash at the beginning or end of an amino acid residue sequence indicates a peptide bond to a further sequence of one or more amino acid residues, to an amino-terminal group such as NH₂ or to a carboxyl-terminal group such as COOH.

As used herein, “naturally occurring amino acids” refer to the 20 L-amino acids that occur in polypeptides.

As used herein, the term “non-natural amino acid” refers to an organic compound that has a structure similar to a natural amino acid but has been modified structurally to mimic the structure and reactivity of a natural amino acid. Non-naturally occurring amino acids thus include, for example, amino acids or analogs of amino acids other than the 20 naturally occurring amino acids and include, but are not limited to, the D-stereoisomers of amino acids. Exemplary non-natural amino acids are described herein and are known to those of skill in the art.

As used herein, nucleic acids include DNA, RNA, and analogs thereof, including protein nucleic acids (PNA) and mixtures thereof. Nucleic acids can be single- or double-stranded. When referring to probes or primers (optionally labeled with a detectable label, such as, a fluorescent or a radiolabel), single-stranded molecules are contemplated. Such molecules are typically of a length such that they are statistically unique of low copy number (typically less than 5, generally less than 3) for probing or priming a library. Generally a probe or primer contains at least 10, 15, 20, 25, or 30 contiguous nucleic acid bases of sequence complementary to, or identical to, a gene of interest. Probes and primers can be 5, 6, 7, 8, 9, 10, or more, 20 or more, 30 or more, 50 or more, 100, or more nucleic acids long.

As used herein, heterologous or foreign nucleic acid, such as DNA and RNA, are used interchangeably and refer to DNA or RNA that does not occur naturally as part of the genome in which it occurs or is found at a locus or loci in a genome that differs from that in which it occurs in nature. Heterologous nucleic acid includes nucleic acid not endogenous to the cell into which it is introduced, but that has been obtained from another cell or prepared synthetically. Generally, although not necessarily, such nucleic acid encodes RNA and proteins that are not normally produced by the cell in which it is expressed. Heterologous DNA herein encompasses any DNA or RNA that one of skill in the art recognizes or considers as heterologous or foreign to the cell or locus in or at which it is expressed. Heterologous DNA and RNA also can encode RNA or proteins that mediate or alter expression of endogenous DNA by affecting transcription, translation, or other regulatable biochemical processes. Examples of heterologous nucleic acid include, but are not limited to, nucleic acid that encodes traceable marker proteins (such as, a protein that confers drug resistance), nucleic acid that encodes therapeutically effective substances (such as, anti-cancer agents), enzymes and hormones, and DNA that encodes other types of proteins (such as, antibodies). Hence, herein heterologous DNA or foreign DNA includes a DNA molecule not present in the exact orientation and position as the counterpart DNA molecule found in the genome. It also can refer to a DNA molecule from another organism or species (i.e., exogenous).

As used herein, “isolated with reference to a nucleic acid molecule or polypeptide or other biomolecule” means that the nucleic acid or polypeptide has separated from the genetic environment from which the polypeptide or nucleic acid were obtained. It also can mean altered from the natural state. For example, a polynucleotide or a polypeptide naturally present in a living animal is not “isolated,” but the same polynucleotide or polypeptide separated from the coexisting materials of its natural state is “isolated,” as the term is employed herein. Thus, a polypeptide or polynucleotide produced and/or contained within a recombinant host cell is considered isolated. Also intended as an “isolated polypeptide” or an “isolated polynucleotide” are polypeptides or polynucleotides that have been partially or substantially purified from a recombinant host cell or from a native source. For example, a recombinantly produced version of a compound can be substantially purified by the one-step method described in Smith et al. (1988) Gene, 67:31-40. The terms isolated and purified can be used interchangeably.

Thus, by “isolated” it is meant that the nucleic acid is free of coding sequences of those genes that, in the naturally-occurring genome of the organism (if any), immediately flank the gene encoding the nucleic acid of interest. Isolated DNA can be single-stranded or double-stranded, and can be genomic DNA, cDNA, recombinant hybrid DNA or synthetic DNA. It can be identical to a starting DNA sequence or can differ from such sequence by the deletion, addition, or substitution of one or more nucleotides.

“Purified” preparations made from biological cells or hosts mean at least the purity of a cell extracts containing the indicated DNA or protein including a crude extract of the DNA or protein of interest. For example, in the case of a protein, a purified preparation can be obtained following an individual technique or a series of preparative or biochemical techniques, and the DNA or protein of interest can be present at various degrees of purity in these preparations. The procedures can include, but are not limited to, ammonium sulfate fractionation, gel filtration, ion exchange chromatography, affinity chromatography, density gradient centrifugation, and electrophoresis.

A preparation of DNA or protein that is “substantially pure” or “isolated” refers to a preparation substantially free from naturally-occurring materials with which such DNA or protein is normally associated in nature and generally contains 5% or less of the other contaminants.

A cell extract that contains the DNA or protein of interest refers to a homogenate preparation or cell-free preparation obtained from cells that express the protein or contain the DNA of interest. The term “cell extract” is intended to include culture medium, especially spent culture medium from which the cells have been removed.

As used herein, “a targeting agent” refers to any molecule that can bind another target-molecule, such as an antibody, receptor, or ligand.

As used herein, “receptor” refers to a biologically active molecule that specifically binds to (or with) other molecules. The term “receptor protein” can be used to more specifically indicate the proteinaceous nature of a specific receptor.

As used herein, “recombinant” refers to any progeny formed as the result of genetic engineering.

As used herein, a “promoter region” refers to the portion of DNA of a gene that controls transcription of the DNA to which it is operatively linked. The promoter region includes specific sequences of DNA sufficient for RNA polymerase recognition, binding, and transcription initiation. This portion of the promoter region is referred to as the “promoter”. In addition, the promoter region includes sequences that modulate this recognition, binding and transcription initiation activity of the RNA polymerase. Promoters, depending upon the nature of the regulation, can be constitutive or regulated by cis acting or trans acting factors.

As used herein, the phrase “operatively linked” with reference to a nucleic acid molecule generally means the sequences or segments have been covalently joined into one piece of DNA, whether in single- or double-stranded form, whereby control or regulatory sequences on one segment control or permit expression or replication or other such control of other segments. The two segments are not necessarily contiguous. For gene expression, a DNA sequence and a regulatory sequence(s) are connected in such a way to control or permit gene expression when the appropriate molecular, such as, transcriptional activator proteins, are bound to the regulatory sequence(s).

As used herein, “production by recombinant means by using recombinant DNA methods” means the use of the well-known methods of molecular biology for expressing proteins encoded by cloned DNA, including cloning expression of genes and methods.

As used herein, a splice variant refers to a variant produced by differential processing of a primary transcript of genomic DNA that results in more than one type of mRNA.

As used herein, a composition refers to any mixture of two or more products or compounds (such as, agents, modulators, regulators, etc.). It can be a solution, a suspension, liquid, powder, a paste, aqueous, non-aqueous formulations or any combination thereof.

As used herein, a combination refers to any association between two or more items.

As used herein, an “article of manufacture” is a product that is made and sold. As used throughout this application, the term is intended to encompass pharmaceutical compositions of modified FIX polypeptides and/or nucleic acids as described herein contained in articles of packaging.

As used herein, a “kit” refers to a combination of modified FIX polypeptides or nucleic acid molecules as described herein provided in pharmaceutical compositions and another item for a purpose including, but not limited to, administration, diagnosis, and assessment of an activity or property of the polypeptides described herein. Kits, optionally, include instructions for use.

As used herein, “substantially identical to a product” means sufficiently similar so that the property of interest is sufficiently unchanged so that the substantially identical product can be used in place of the product.

As used herein, vector (or plasmid) refers to discrete elements that are used to introduce heterologous DNA into cells for either expression or replication thereof. Selection and use of such vehicles are well within the skill of the artisan. “Vector” refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. One type of exemplary vector is an episome, i.e., a nucleic acid capable of extra-chromosomal replication. Exemplary vectors are those capable of autonomous replication and/or expression of nucleic acids to which they are linked; such vectors typically include origins of replication. Vectors also can be designed for integration into host chromosomes. Vectors capable of directing the expression of genes to which they are operatively linked are referred to herein as “expression vectors.” Expression vectors are often in the form of “plasmids,” which refer generally to circular double-stranded DNA loops which, in their vector form are not bound to the chromosome. “Plasmid” and “vector” are used interchangeably as the plasmid is the most commonly used form of vectors. Other such forms of expression vectors that serve equivalent functions and that become known in the art subsequently hereto.

As used herein, vector also includes “virus vectors” or “viral vectors.” Viral vectors are engineered viruses that are operatively linked to exogenous genes to transfer (as vehicles or shuttles) the exogenous genes into cells.

As used herein, “allele,” which is used interchangeably herein with “allelic variant” refers to alternative forms of a gene or portions thereof among a population. Alleles occupy the same locus or position on homologous chromosomes. When a subject has two identical alleles of a gene, the subject is said to be homozygous for that gene or allele. When a subject has two different alleles of a gene, the subject is said to be heterozygous for the gene. Alleles of a specific gene can differ from each other in a single nucleotide or several nucleotides, and can include substitutions, deletions, and insertions of nucleotides. An allele of a gene also can be a form of a gene containing a mutation. Typically, allelic variants, have at least 80%, 90%, 95% or greater amino acid identity with a wild-type and/or predominant form from the same species.

As used herein, the terms “gene” or “recombinant gene” refer to a nucleic acid molecule containing an open reading frame and including at least one exon and, optionally, an intron-encoding sequence. A gene can be either RNA or DNA. Genes can include regions preceding and following the coding region (leader and trailer).

As used herein, “intron” refers to a DNA fragment that occurs in a gene, but that is spliced out during mRNA maturation.

As used herein, “nucleotide sequence complementary to the nucleotide sequence encoding the amino acid sequence set forth in SEQ ID NO: 1” refers to the nucleotide sequence of the complementary strand of a nucleic acid strand encoding a polypeptide that includes an amino acid sequence having the particular SEQ ID NO: 1. An exemplary nucleic acid sequence that encodes an amino acid sequence having the particular SEQ ID NO: 1 is set forth in SEQ ID NO: 897.

The term “complementary strand” is used herein interchangeably with the term “complement.” The complement of a nucleic acid strand can be the complement of a coding strand or the complement of a non-coding strand. When referring to double-stranded nucleic acids, the complement of a nucleic acid encoding a polypeptide containing amino acid residues having a sequence set forth in a particular SEQ ID NO: 1 refers to the complementary strand of the strand encoding the amino acid sequence set forth in the particular SEQ ID NO: 1 or to any nucleic acid molecule containing the nucleotide sequence of the complementary strand of the particular nucleic acid sequence. When referring to a single-stranded nucleic acid molecule containing a nucleotide sequence, the complement of this nucleic acid is a nucleic acid having a nucleotide sequence which is complementary to that of the particular nucleic acid sequence.

As used herein, the term “coding sequence” refers to that portion of a gene that encodes a sequence of amino acids present in a protein.

As used herein, the term “sense strand” refers to that strand of a double-stranded nucleic acid molecule that has the sequence of the mRNA that encodes the sequence of amino acids encoded by the double-stranded nucleic acid molecule.

As used herein, the term “antisense strand” refers to that strand of a double-stranded nucleic acid molecule that is the complement of the sequence of the mRNA that encodes the sequence of amino acids encoded by the double-stranded nucleic acid molecule.

As used herein, an “array” refers to a collection of elements, such as nucleic acid molecules, containing three or more members. An addressable array is one in which the members of the array are identifiable, typically by position on a solid phase support or by virtue of an identifiable or detectable label, such as by color, fluorescence, electronic signal (i.e., RF, microwave or other frequency that does not substantially alter the interaction of the molecules of interest), bar code or other symbology, chemical or other such label. In certain embodiments, the members of the array are immobilized to discrete identifiable loci on the surface of a solid phase or directly or indirectly linked to or otherwise associated with the identifiable label, such as affixed to a microsphere or other particulate support (herein referred to as beads) and suspended in solution or spread out on a surface.

As used herein, a “support” (such as, a matrix support, a matrix, an insoluble support or solid support, etc.) refers to any solid or semisolid or insoluble support to which a molecule of interest (such as, a biological molecule, organic molecule or biospecific ligand) is linked or contacted. Such materials include any materials that are used as affinity matrices or supports for chemical and biological molecule syntheses and analyses, such as, but are not limited to: polystyrene, polycarbonate, polypropylene, nylon, glass, dextran, chitin, sand, pumice, agarose, polysaccharides, dendrimers, buckyballs, polyacrylamide, silicon, rubber, and other materials used as supports for solid phase syntheses, affinity separations and purifications, hybridization reactions, immunoassays and other such applications. The matrix herein can be particulate or can be in the form of a continuous surface, such as a microtiter dish or well, a glass slide, a silicon chip, a nitrocellulose sheet, nylon mesh, or other such materials. When particulate, typically the particles have at least one dimension in the 5-10 mm range or smaller. Such particles, referred collectively herein as “beads,” are often, but not necessarily, spherical. Such reference, however, does not constrain the geometry of the matrix, which can be any shape, including random shapes, needles, fibers, and elongated. Roughly spherical “beads,” particularly microspheres that can be used in the liquid phase, also are contemplated. The “beads” can include additional components, such as magnetic or paramagnetic particles (see, for example, Dynabeads (Dynal, Oslo, Norway)) for separation using magnets as long as the additional components do not interfere with the methods and analyses herein.

As used herein, matrix or support particles refer to matrix materials that are in the form of discrete particles. The particles have any shape and dimensions, but typically have at least one dimension that is 100 mm or less, 50 mm or less, 10 mm or less, 1 mm or less, 100 μm or less, 50 μm or less and typically have a size that is 100 mm³ or less, 50 mm³ or less, 10 mm³ or less, 1 mm³ or less, 100 μm³ or less and can be order of cubic microns. Such particles are collectively called “beads.”

As used herein, the abbreviations for any protective groups, amino acids and other compounds are, unless indicated otherwise, in accord with their common usage, recognized abbreviations, or the IUPAC-IUB Commission on Biochemical Nomenclature (1972) Biochem., 11: 942-944.

B. HEMOSTASIS OVERVIEW

Provided herein are modified FIX polypeptides. These modified polypeptides have a variety of uses and applications. To appreciate the biological role of FIX polypeptides and some of their uses, an understanding of their role function in vivo is helpful. The following discussion provides such background.

The process by which the body responds to vascular injury involves a series of dependent signaling events that ultimately leads to the formation of a blot clot. Effective coagulation of blood is needed to prevent excessive blood loss at the site of injury. Once a blood vessel is injured or ruptured, vascular constriction, which limits blood flow to the area of the injury, accompanies the initial physiologic response. The rupture exposes highly thrombogenic subendothelial connective tissue that is composed of fibrillar collagen, which binds and activates platelets and stimulates platelet aggregation at the injury site. The activated platelets secrete factors which stimulate additional platelet activation, and other molecules, such as serotonin, phospholipids, and lipoproteins, which are important mediators of the clotting process. Fibrinogen, a component of the blood plasma also binds platelets and aids in clumping of the activated platelets. The activated platelets in turn undergo changes in cell shape to form a loose platelet plug. A clotting cascade of peptidases is simultaneously initiated that generates activated molecules such as thrombin (from cleavage of prothrombin), which further activates platelets, and fibrin (from cleavage of fibrinogen), which forms a cross-linked polymer around the platelet plug to stabilize the clot. During clot formation, coagulation factor inhibitors also circulate through the blood to prevent clot formation beyond the injury site.

Following repair of the injured tissue, the body must efficiently dissolve the clot in order to restore normal blood flow. Fibrinolysis is the process by which the clotting cascade is reduced and the clot is eliminated. Dissolution of the clot is mediated by the protein plasmin.

The processes of clot initiation, signal amplification, and fibrinolysis, and the factors involved are presented in further detail below.

1. Clot Initiation

Under normal conditions, vascular endothelium is resistant to clot formation. This resistance is supported by mechanisms that enhance vasodilation, inhibit platelet adhesion and activation, suppress coagulation, and promote fibrin cleavage. Vascular endothelial cells secrete molecules such as nitrous oxide (NO) and prostacylin, which inhibit platelet aggregation and dilate blood vessels. Release of these molecules activates soluble guanylate cyclases (sGC) and cGMP-dependent protein kinase I (cGKI) and increases cyclic guanosine monophosphate (cGMP) levels, which cause relaxation of the smooth muscle in the vessel wall. Furthermore, endothelial cells express cell-surface ADPases, such as CD39, which control platelet activation and aggregation by converting ADP released from platelets into adenine nucleotide platelet inhibitors. Other membrane proteins expressed on the surface of vascular endothelial cells include heparin sulfate proteoglycans that function as cofactors for antithrombin III, which inhibits thrombin and other coagulation factors. In addition, vascular endothelial cells secrete plasminogen to promote fibrinolysis, which lyses and clears clots.

Upon blood vessel injury, the damaged vessel wall exposes the subendothelial connective tissue to the circulating blood. In contrast to normal endothelial cells, this tissue is extremely thrombogenic. The layer is composed of proteins such as von Willebrand factor (vWF) and fibrillar collagen, which bind to circulating platelets via glycoprotein receptors expressed on the surface of the platelets. The platelet glycoprotein receptor complex GPIb-V-IX binds vWF, whereby vWF can bridge the platelets to the collagen fibrils. vWF is a multimeric glycoprotein, which contributes to its ability to aggregate platelets. vWF also functions to stabilize coagulation factors, such as factor VIII, and promotes their survival in the blood stream. Furthermore, the platelet integrin receptors α₂β₁ and GPVI can bind to collagen directly. Binding of collagen to α₂β₁ can facilitate binding to the lower affinity GPVI receptor. The collagen interactions with α₂β₁ and GPVI contribute to platelet adherence to the site of injury and furthermore promote platelet activation through activation of intracellular signaling cascades.

2. Signal Amplification and the Clotting Cascade

During clot formation, positive feedback loops are activated that enhance the maturation of a clot. Following platelet activation, expression of the platelet surface integrin α_(IIb)β₃ is stimulated. α_(IIb)β₃ can bind to vWF and fibrinogen. Binding of GPIb-V-IX to vWF can enhance the affinity of α_(IIb)β₃ for vWF to promote platelet adhesion. Further, one fibrinogen molecule can bind to multiple α_(IIb)β₃ integrin molecules from different cells, thus, enhancing platelet aggregation.

Platelet activation stimulates the release of platelet alpha and dense granules. The released contents of the granules include factors, such as vWF and ADP, which further contribute to aggregation and platelet activation. ADP helps stimulate modification of the platelet membrane that allows binding of fibrinogen to α_(IIb)β₃, and vWF contributes to adhesion and aggregation as discussed above.

In addition to ADP, activated platelets also secrete factors such as serotonin and thromboxane A₂ (TXA₂) which also positively regulate platelet activation. Signal transduction cascades activated in response to thrombin binding control release of these factors. During platelet activation, thrombin binds to a G-protein coupled receptor on the surface of platelets. The receptor becomes stimulated, and the activated G-protein activates phospholipase C-γ 2 (PLCγ2), which hydrolyzes phosphatidylinositol 4,5-bisphosphate (PIP₂) to generate inositol triphosphate (IP₃) and diacylglycerol (DAG). IP₃ stimulates release of intracellular calcium (Ca²⁺) stores from the endoplasmic reticulum by binding to IP₃ receptors. The released calcium in combination with collagen binding to platelets leads to the activation of phospholipase A2 (PLA₂). PLA₂ then hydrolyzes membrane phospholipids, such as phosphatidylcholine (PC) and phosphatidylethanolamine (PE), to generate arachidonic acid, which in turn stimulates the production and release of TXA₂.

The production of DAG by activated platelets stimulates protein kinase C, which then phosphorylates a platelet specific 47 kDa protein (p47). The phosphorylated p47 protein induces the release of the platelet granules as discussed above. Intracellular Ca²⁺ release also activates myosin light chain kinase (MLCK) that phosphorylates the light chain of myosin. The phosphorylated myosin then interacts with actin, bringing about a change in platelet morphology and motility, necessary for clot formation.

Platelet activation through collagen binding also elicits activation of a similar signaling cascade. When collagen binds to the GPVI integrin, it promotes clustering of GPVI with the Fc receptor γ-chain (FcγR). The clustering induces tyrosine phosphorylation of the FcγR by Src-family kinases Lyn and Fyn, which promote binding and activation of the tyrosine kinase Syk. Syk, in turn phosphorylates the transmembrane adapter protein LAT, which then assembles a signaling complex composed of proteins including phosphoinositide 3-kinase (PI3K), PLCγ2, adaptor proteins such as Gads, SLP-75, and SLAP-130, and the RhoGTP exchange factor Vav. PI3K can then regulate protein kinase B (PKB), phosphoinositide-dependent kinase (PDK1) and integrin-linked kinase (ILK), which can regulate integrin expression and signaling. PLCγ2 generates IP₃ and DAG to mobilize calcium and activate PKC as described above.

For stable clot formation, cross-linked fibrin polymers must be formed surrounding the activated platelet plug. Fibrin formation is generated though activation of coagulation factor cascades which occurs simultaneously with platelet activation, following vessel injury. Two converging pathways can be activated, the intrinsic and extrinsic pathway. Key factors that participate in the intrinsic and extrinsic coagulation cascades are listed in Tables 2 and 3. The high-molecular weight kininogen, prekallikrein, and factors XII, XI, IX, and VIII participate in the intrinsic pathway, while tissue factor and the factor VII complex contribute to the extrinsic pathway. The two pathways converge at the activation of factor X (to generate FXa), through proteolytic action of the activated factor IX (FIXa)/factor VIII (FVIIIa) tenase complex (intrinsic) or by the activated factor VII (FVIIa)/tissue factor (TF) complex (extrinsic). Activated factor X (FXa), with the help of factor V, calcium, and platelet phospholipid, generates thrombin from prothrombin. In turn, thrombin cleaves fibrinogen to produce fibrin and also activates factor XIII (transglutamidase), which cross-links fibrin polymers to form the stable clot. The surface of activated platelets facilitates the formation of the activated coagulation factor complexes and thus participates in amplification of the cascade.

The primary pathway for initiation is the extrinsic pathway; the intrinsic pathway functions to amplify the production of activated factor X. Following vascular injury, tissue factor (TF) in the vessel wall is exposed and generated. TF is expressed by endothelial cells, subendothelial tissue, and monocytes. When the vessel wall is disrupted TF produced by the subendothelial layer is exposed. In the case of endothelial cell damage in the absence of a vessel wall lesion, contact is made between the blood and TF expressed on the damaged endothelial layer in the cell wall. vWF aids in the interaction of platelets with the damaged endothelium. TF binds to VII and in turn catalyzes the activation of factor X. The thrombin that is generated by the extrinsic pathway then contributes to activation of factor XI of the intrinsic cascade, leading to the activation of factor IX. Factor IX also can be activated directly by the TF/factor VII complex. The intrinsic cascade also can be activated via factor XII-mediated activation of factor XI when prekallikrein is converted to kallikrein in response to collagen contact with the vessel surface (called the contact pathway), though this pathway plays a minimal role in coagulation as compared to the amplification effects of thrombin. The contact pathway plays a more important role in fibrinolysis since factor XII and kallikrein can convert plasminogen into plasmin and bradykinin, which is a potent vasodilator and stimulator for tissue plasminogen activator (tPA).

3. Termination of Coagulation and Fibrinolysis

During coagulation constitutive and stimulated processes inhibit further clot formation. Antithrombin III and tissue factor pathway inhibitor (TFPI) work constitutively to inhibit factors in the coagulation cascade. Specifically, antithrombin III inhibits thrombin, FIXa, and FXa, where as TFPI inhibits FXa and FVIIa/TF complex. Protein C, which is stimulated via platelet activation, proteolytically inactivates FVa and FVIIIa. Further, another factor which contributes to coagulation inhibition is the integral membrane protein thrombomodulin, which is produced by vascular endothelial cells and binds thrombin. Complex formation inhibits thrombin procoagulant activities and also contributes to protein C activation.

Clearance of the fibrin clot is carried out by the serine protease plasmin, which can digest fibrin. Prior to activation of this enzyme, it circulates in the blood in the form of the proenzyme plasminogen. Plasminogen can bind to fibrin and fibrinogen, which allows it to be incorporated into the clot as it is formed. Cleavage of plasminogen into active plasmin is primarily carried out by activated tPA, which is secreted by endothelial cells following injury, through stimulation of tPA activity. Production of plasmin also can be initiated and enhanced by the actions of factor XII as discussed above.

TABLE 2 Coagulation Factors Factor Common Name Pathway Characteristic I Fibrinogen Both — II Prothrombin Both Contains N-terminal gla segment III Tissue Factor Extrinsic — IV Calcium Both — V Proaccelerin, labile factor, Both Protein cofactor Accelerator globulin VI Accelerin — (Redundant to factor V) (Va) VII Proconvertin, serum prothrombin Extrinsic Endopeptidase with conversion accelerator (SPCA) gla residues cothromboplastin VIII Antihemophiliac factor A, Intrinsic Protein cofactor antihemophiliac globulin (AHG) IX Christmas factor, antihemophiliac Intrinsic Endopeptidase with factor B, plasma thromboplastin gla residues component (PTC) X Stuart-prower factor Both Endopeptidase with gla residues XI Plasma thromboplastin Intrinsic Endopeptidase antecedent (PTA) XII Hageman factor Intrinsic Endopeptidase XIII Protransglutamidase, fibrin Both Transpeptidase stabilizing factor (FSF), fibrinoligase *Table adapted from M. W. King (2006) med.unibs.it/~marchesi/blood.html

TABLE 3 Coagulation Factor Zymogens and Cofactors Name of Factor Activity Zymogens of Serine Proteases Factor XII Binds exposed collagen at site of vessel wall injury, activated by high-MW kininogen and kallikrein Factor XI Activated by factor XIIa Factor IX Activated by factor XIa + Ca²⁺ Factor VII Activated by thrombin + Ca²⁺ Factor X Activated on platelet surface by tenase complex; Also activated by factor VIIa + tissue factor + Ca²⁺ Factor II Activated on platelet surface by prothrombinase complex; Cofactors Factor VIII Activated by thrombin; factor VIIa acts as cofactor for factor IXa in activation of factor X Factor V Activated by thrombin; factor Va acts as cofactor for factor Xa in activation of prothrombin Factor III (Tissue factor) Acts as cofactor for factor VII Fibrinogen Factor I Cleaved by thrombin to form fibrin Transglutaminase Factor XIII Activated by thrombin + Ca²⁺; promotes covalent cross-linking of fibrin Regulatory and other proteins von Willebrand factor (vWF) Acts as bridge between GPIb-V-IX complex and collagen Protein C Activated by thrombin bound to thrombomodulin; Ca degrades factors VIIIa and Va Protein S Acts as cofactor of protein C Thrombomodulin Endothelial cell surface protein; binds thrombin, which activates protein C Antithrombin III Coagulation inhibitor of thrombin, and factors IXa, Xa, XIa, and XIIa. *Table adapted from M. W. King (2006) med.unibs.it/~marchesi/blood.html

C. FACTOR IX (FIX)

Coagulation Factor IX (FIX) is a vitamin-K dependent serine protease produced in animals, including mammals, that plays a pivotal role in the blood clotting cascade that functions to seal injured blood vessels. FIX shows a high degree of homology to other vitamin-K dependent serine proteases, including factor VII, factor X, and protein C (Furie et al., 1988). FIX is synthesized in the liver as an inactive zymogen that is secreted into the blood stream. During the coagulation process, FIX is cleaved via the intrinsic pathway by active factor XIa to generate an active serine protease, FIXa. FIXa also is generated via the extrinsic pathway by factor VIIa/tissue factor (FVIIa/TF). FIXa binds to activated Factor VIII (FVIIIa) and catalyzes the conversion of factor X to its active form, factor Xa, which hydrolyzes prothrombin into active thrombin

Coagulation factors, including FIX, are used as therapeutic agents. Treatment with recombinant FIX is an established therapy. Recombinant FIX is used, for example, as a therapeutic for treatment of diseases such as hemophilia, in particular, hemophilia B. Patients receiving FIX are subject to frequent, repeated applications of the drug due to instability of FIX in the blood stream and under storage conditions. Hence, improved FIX stability (half-life) in serum or following oral administration and/or in in vitro applications can improve its activity and efficiency as a drug. Accordingly, provided herein are modified FIX polypeptides that display improved protein stability, such as by increased resistance to proteases, resulting in increased protein half-life. The modified polypeptides can possess increased stability in the bloodstream or following oral administration (in vivo) and/or under storage conditions (in vitro).

1. Factor IX Structure and Function

The human coagulation FIX gene is located on chromosome X at Xq27.1 and contains 8 exons of varying length from 25 base pairs to about 2000 base pairs. The mRNA for FIX is about 3 kilobases in length, comprising 205 bases of 5′ UTR (untranslated region), 1386 bases encoding the FIX polypeptide, and 1392 bases of 3′ UTR. The FIX mRNA encodes for a 461 amino acid precursor FIX polypeptide. The nucleotide coding sequence and the encoded precursor polypeptide are provided in SEQ ID NOS: 897 and 1, respectively.

The precursor FIX polypeptide comprises the following segments and domains: a hydrophobic signal peptide (aa 1-28 of SEQ ID NO: 1), a propeptide (aa 29-46 of SEQ ID NO: 1), a gla domain (aa 47-92 of SEQ ID NO: 1), a type B epidermal growth factor domain (EGF-like 1, aa 93-129 of SEQ ID NO: 1), a type A epidermal growth factor domain (EGF-like 2, aa 130-171 of SEQ ID NO: 1), an activation peptide (aa 192-226 of SEQ ID NO: 1), and a serine protease domain (aa 227-461 of SEQ ID NO: 1). The mature form of the FIX polypeptide lacks the signal peptide and propeptide sequences (SEQ ID NO: 2). In the mature form of the FIX polypeptide the corresponding amino acid positions for the above mentioned domains are as follows: gla domain (aa 1-46 of SEQ ID NO: 2), EGF-like 1 (aa 47-83 of SEQ ID NO: 2), EGF-like 2 (aa 84-125 of SEQ ID NO: 2), activation peptide (aa 146-180 of SEQ ID NO: 2), and serine protease domain (aa 181-415 of SEQ ID NO: 2). Amino acid positions for FIX polypeptides provided herein are given with respect to the mature form of the FIX polypeptide (SEQ ID NO: 2), unless otherwise noted.

The signal peptide at the N-terminus of the precursor FIX polypeptide (SEQ IS NO: 1) is 28 amino acids in length and functions to target the FIX polypeptide to the cellular secretory pathway by insertion into the endoplasmic reticulum (ER) during translation. The signal sequence is cleaved by a signal peptidase within the ER lumen. Once inside the ER lumen, the FIX polypeptide is post-translationally modified by N-linked and O-linked glycosylation, β-hydroxylation, and γ-carboxylation. β-hydroxylation and γ-carboxylation are completed in the ER, while glycosylation commences in the ER and finishes in the Golgi complex.

The propeptide, which is 18 amino acids in length, provides a binding site for a vitamin K-dependent carboxylase. The recognition element for the carboxylase is located in the N-terminal portion of the propeptide, which forms a 10 residue amphipathic α-helix. After binding, the carboxylase γ-carboxylates 12 glutamic acid residues within the gla domain of the FIX polypeptide, producing γ-carboxyglutamyl residues at positions E53, E54, E61, E63, E66, E67, E72, E73, E76, E79, E82, and E86 relative to the FIX precursor amino acid sequence set forth in SEQ ID NO: 1. These positions correspond to positions E7, E8, E15, E17, E20, E21, E26, E27, E30, E33, E36, and E40 relative to the mature FIX polypeptide set forth in SEQ ID NO: 2. The γ-carboxyglutamyl modifications aid in the correct folding of the mature FIX polypeptide and in the ability to FIX to bind calcium (Ca²⁺) and phospholipids. γ-Carboxyglutamyl residues located at amino acid positions 17, 21, and 27, relative to the mature FIX polypeptide (SEQ ID NO: 2), form ion pairs with the amino terminal alanine in prothrombin, which stabilize the structure of the gla domain and promote interaction with phospholipid membranes (Soriano-Garcia et al. (1992) Biochemistry 31:2554-2566). The C-terminal end of the gla domain also contains a conserved hydrophobic domain containing a Phe-Trp-X-X-Tyr motif, located at amino acid positions 41-45 relative to the mature FIX polypeptide (SEQ ID NO: 2), which is required for Ca²⁺ dependent changes in protein structure and for formation of a membrane binding site with the gla domain. In addition, proper folding of the gla domain enables binding of cofactor FVIIIa to FIXa, in order to form the complex which catalyzes the conversion of factor X into its active form, FXa. With respect to the other post-translational modifications of FIX, β-hydroxylation occurs at D64 to form β-hydroxyaspartic acid, N-linked glycosylation at N157 and N167, O-linked glycosylation at S53, S61, T159, T169, T172, and T179; sulfation at Y155; and phosphorylation of S68 and S158, relative to the mature FIX polypeptide, SEQ ID NO: 2 (Furie et al. (1988) Cell 53:505-518 and Kaufman et al. (1998) Thromb. Haemost 79:1068-1079).

After post-translation modification and prior to secretion, the propeptide is cleaved by a propeptidase to generate the mature FIX polypeptide, which is 415 amino acids in length (SEQ ID NO: 2). The recognition element for binding of the propeptidase is proposed to be located on the carboxyl side of the propeptide, closer to the site of cleavage. PACE/furin is a subtilisin-like calcium-dependent serine propeptidase localized to the trans Golgi compartment that has the ability to cleave the FIX propeptide into its mature form (Wasley et al. (1993) J Biol Chem. 268(12):8458-65). The name PACE is an acronym for Paired basic Amino acid Cleaving Enzyme, which describes the characteristic of the enzyme to cleave after a pair of basic amino acids, namely K45-R46 in FIX (positions relative to precursor FIX polypeptide as set forth in SEQ ID NO: 1; K-2 and R-1 relative to the mature FIX polypeptide set forth in SEQ ID NO: 2). The consensus motif for PACE cleavage is Arg-X-(Lys/Arg)-Arg. PACE/furin also functions to process the propeptides of other proteins, such as pro-von Willebrand factor, pro-nerve growth factor proalbumin, and complement pro-C3. PACE/furin is ubiquitously expressed and is likely to process additional proteins, including growth factors, receptors, and other coagulation factors. Other members of the PACE family of peptidases include PC1/3, PC2, PACE4, PC4, PC5/6 and PC7/SPC7/LPC/PC8, though functional and expression data suggest that PACE/furin is most likely the FIX propeptidase in vivo. Mutation of the tyrosine residue at position 1 of the mature FIX polypeptide (Y47 in the precursor FIX polypeptide) has been shown to increase the efficiency of cleavage of the propeptide sequence (Meulian et al. (1990) Protein Eng. 3(7):629-33).

The first EGF-like domain (EGF-like 1, EGF 1) is a type B EGF domain and contains the β-hydroxylation site at D64. β-Hydroxylation aids in the binding of additional Ca²⁺, which promotes binding of cofactor VIII to the domain. Two O-linked glycosylation sites are located within this domain at S53 and S61 (relative to the mature FIX polypeptide, SEQ ID NO: 2).

The second EGF-like domain (EGF-like 2, EGF2) is a type A EGF domain, which lacks β-hydroxylated residues compared to the type B domain. The EGF2 domain is responsible for binding to platelets and for assembly of the factor X activating complex (Wilkinson et al. (2002) J. Biol. Chem., 277(8):5734-5741). Formation of this complex on the surface of activated platelets promotes efficient hydrolysis of factor X.

The activation peptide contains the two cleavage sites, R145-A146 and R180-V181 (relative to mature FIX polypeptide, SEQ ID NO: 2) which are hydrolyzed by FXIa in the presence of Ca²⁺, or by FVIIa in the presence of TF, phospholipid, and Ca²⁺ to generate the activated form, FIXa. The activation peptide also contains two of the N-linked glycosylation sites at N157 and N167 and four of the O-linked glycosylation sites at T159, T169, T172, and T179. Upon cleavage, the activation peptide (SEQ ID NO: 895) is excised from the polypeptide, leaving the activated FIX polypeptide, containing of a light chain and a heavy chain that are attached via cysteine disulfide bonds. The light chain includes the amino terminal portion of the FIX polypeptide, comprising the gla, EGF1, and EGF2 domains (SEQ ID NO: 894). The heavy chain comprises the FIX serine protease domain (SEQ ID NO: 896).

The serine protease domain is a catalytic domain that is homologous to known serine proteases, such as chymotrypsin, and contains an analogous catalytic core of residues at H221, D269, and S365 (relative to the mature FIX polypeptide, SEQ ID NO: 2). The protease domain catalyzes the hydrolysis of factor X in the presence of Ca²⁺, phospholipids, and FVIIIa by cleaving the R53-I53 bond of mature factor X.

2. Factor IX Polypeptides

Factor IX (FIX) polypeptides are heterogeneous polypeptides, are made of varying amino acid sequence lengths and include, but are not limited to, recombinantly produced polypeptide, synthetically produced polypeptide and FIX extracted from cells as tissues such as, for example, liver. FIX includes related polypeptides from different species including, but not limited to, animals of human and non-human origin, allelic variant isoforms, species isoforms, synthetic molecules from nucleic acids, protein isolated from human tissue and cells, and modified forms thereof. Exemplary unmodified mature FIX polypeptides include, but are not limited to, unmodified and wild-type native FIX polypeptide (such as the polypeptide containing a sequence set forth in SEQ ID NO: 2), the unmodified and wild-type precursor FIX polypeptide that includes a signal peptide and a propeptide (such as the polypeptide that has the sequence set forth in SEQ ID NO: 1), a polymorphic wild-type variant of native factor IX polypeptide that has alanine at amino acid position T148 (SEQ ID NO: 892; or its precursor containing a sequence of amino acids set forth in SEQ ID NO: 893), and chimeric variants of FIX polypeptides such as set forth in SEQ ID NO: 1035. Unmodified FIX polypeptides also include FIX polypeptides that are modified by the cellular machinery and include, for example, glycosylation, carboxylation, β-hydroxylation, sulfation, and phosphorylation.

Based on alignment of FIX with other coagulation factor family members, such as factor VII (FVII) or factor X (FX), homologous domains among the family members are readily identified. Chimeric variants of FIX polypeptides can be constructed where one or more amino acids or entire domains are replaced in the FIX amino acid sequence using the amino acid sequence of the corresponding family member. Such chimeric proteins can be used as the unmodified FIX polypeptide for the methods described herein. For example, amino acid residues of the gla domain can be replaced with residues from the analogous FVII or FX gla domains (Lin et al. (1990) J. Biol. Chem. 265(1):144-150 and Cheung et al. (1991) J. Biol. Chem. 266(14):8797-880). A chimeric FIX protein can then be further modified by amino acid replacement for increased protein stability using any the methods described herein. Exemplary modified chimeric FIX polypeptides have amino acid sequences set forth in SEQ ID NOS: 1036-2044.

FIX is functionally active following cleavage by FXIa in the presence of Ca²⁺ or by FVIIa in the presence of TF, phospholipid, and Ca²⁺. Hydrolysis of mature FIX polypeptides generates heavy and light chains of FIX that are connected by disulfide bridges. FIX polypeptides therefore also include FIX heavy chain and FIX light chain polypeptides (SEQ ID NOS: 896 and 894, respectively) and combinations thereof.

The full structure of coagulation FIX is formed from six FIX molecules. Modified polypeptides can be stabilized by intra- (within FIX polypeptide) and inter- (between heavy and light chains of FIX polypeptide or between subunits) subunit interactions. Amino acids within the helices of each FIX polypeptide chain can interact with each other, thereby contributing to protein stability within a FIX polypeptide (i.e., “intrastability”). For example, cysteine residues form disulfide bonds between the FIX heavy and light polypeptide chains. In addition, interhelical contacts occur between helices of different subunits thereby contributing to protein stability between the monomers (i.e., “interstability”). For example, amino acid residues in helices on monomer A can interact with amino acid residues in helices on monomer B.

Contemplated herein are modified FIX polypeptides that differ from unmodified or wild-type FIX polypeptides with respect to a property or an activity. Modified FIX polypeptides provided herein can have increased stability, as manifested as increased serum half-life or increased resistance to proteases as compared to unmodified FIX polypeptides.

Generally, FIX is produced as a larger polypeptide (461 aa, SEQ ID NO: 1, for example) that is matured to a smaller polypeptide upon cleavage of the signal sequence (amino acids 1-28 of SEQ ID NO: 1, for example). FIX polypeptides are typically about 433 amino acids in length after cleavage of the signal sequence, and typically about 415 amino acids in length following further cleavage of the propeptide sequence, resulting in a mature FIX polypeptide (SEQ ID NO: 2, for example).

FIX is a secreted, glycosylated protein, including O- and N-linked glycosylation sites. The extent of glycosylation of the FIX polypeptides provided herein can contribute to the stability of the protein and to protease resistance. Glycosylation of FIX polypeptides provided herein also can contribute to the amount of protein expression, secretion, and potency of the FIX polypeptide. FIX polypeptides provided herein can be γ-carboxylated, β-hydroxylated, tyrosine sulfated, and/or phosphorylated.

FIX polypeptides from different species share conserved sequences of amino acids (see, for example, mouse, rat, guinea pig, cow, sheep, dog, cat, chicken, pig, rabbit, fish, and chimpanzee FIX polypeptides). Such sequences can be used for modification using the methods described herein.

Active and inactive forms of FIX polypeptides are known in the art. Active peptidase forms of FIX can be used in the treatment of hemophilias, where FIX polypeptides can function to promote blood coagulation. FIX polypeptides that have an inactive protease domain can be used in the treatment of thrombotic diseases by inhibiting blood coagulation via interference of the coagulation cascade.

Modes of administration include, but are not limited to, FIX polypeptide injection or the nucleic acid molecules encoding modified FIX polypeptides provided herein and also can include additional treatments administered similarly or through other routes of administration, including oral administration and inhalation, stem cell engraftment, and systemic administration of viral vectors encoding a FIX polypeptide. FIX also can be targeted for delivery into specific cell types. For example, adenoviral vectors encoding FIX polypeptides can be used for stable expression in nondividing cells, such as liver cells, and skeletal muscle cells (Arruda et al. (2001) Blood 97(1): 130-138 and Yao et al. (1992) PNAS 89: 3357-3361). In another example, viral or nonviral vectors encoding FIX polypeptides can be transduced into isolated cells for subsequent delivery. Additional cell types for expression and delivery of FIX are known in the art and include but are not limited to, fibroblasts and endothelial cells (Palmer et al. (1989) Blood 73: 438-445; Yao et al. (1991) PNAS 88: 8101-8105).

3. FIX as a Pharmaceutical

Activities induced by FIX include, but are not limited to, blood coagulation. Administration of FIX has been shown to promote blood clotting in patients suffering from hemophilia, particularly hemophilia B. In man, treatment with doses of FIX have been found to be safe and well-tolerated.

FIX can be administered orally, systemically, buccally, transdermally, intravenously, intramuscularly and subcutaneously and, typically, multiple administrations are used in treatment regimens. The formulations are typically stored in refrigerated (2-8° C.) conditions to ensure retention of activity. Hence, improved FIX stability (half-life) in administered conditions (in vivo), such as stability in serum, and in vitro (such as, during production, purification and storage conditions) can improve its utility and efficiency as a drug.

Provided herein are variants of the FIX polypeptide that display improved stability as assessed by resistance to proteases (blood, intestinal, etc) and/or increased thermal tolerance and/or pH conditions, wherein the mutant variants exhibit increased protein half-life. The mutant variants that exhibit improved stability possess increased stability in administration conditions such as in the bloodstream, gastrointestinal tract, under low pH conditions (such as, the stomach), mouth, throat, and/or under storage conditions.

D. EXEMPLARY METHODS FOR MODIFYING FIX

Provided herein are methods for increasing stability and half-life of a FIX polypeptide by increasing resistance to proteolysis. Provided herein are methods of modifying FIX polypeptides to increase resistance to proteolysis by proteases (blood, serum, gastrointestinal, etc.), whereby the modified polypeptide exhibits increased half-life in vitro and/or in vivo. Provided herein are modified FIX polypeptides in which the primary amino acid sequence is modified to confer increased protein stability. Among the amino acid modifications provided herein are such modifications including replacement of amino acids in the primary sequence of the FIX polypeptide in order to decrease proteolytic cleavage of the FIX polypeptide. Further modifications of the modified FIX polypeptide can be included, such as, but not limited to, addition of carbohydrate, phosphate, sulfur, hydroxyl, carboxyl, and polyethylene glycol (PEG) moieties. Thus, the modified FIX polypeptides provided herein can be further modified, for example, by glycosylation, phosphorylation, sulfation, hydroxylation, carboxylation, and/or PEGylation. Such modifications can be performed in vivo or in vitro.

Provided herein are methods of modifying polypeptides to increase resistance to proteolysis by proteases and contacting proteolytic enzymes with peptide inhibitors, thereby inhibiting activity of the proteases. Also provided herein are the modified polypeptides generated by said methods. Provided herein are FIX polypeptides that display improved stability as assessed by resistance to proteases; the modified FIX polypeptides exhibiting these properties possess, thereby, increased protein half-life in vitro or in vivo.

The modified FIX polypeptides (also referred to herein as variants) are more stable compared to unmodified FIX polypeptides. Increasing stability (i.e., the half-life of proteins in vivo) can result in a decrease in the frequency of injections needed to maintain a sufficient drug level in serum, thus leading to: i) higher comfort to, and acceptance by, treated subjects, particularly human subjects, ii) lower doses necessary to achieve comparable biological effects, and iii) as a consequence, an attenuation of the (dose-dependent) secondary effects.

Increased stability of FIX can be achieved, for example, by destruction of protease target residues or sequences and/or by modification of residues that contribute to conformational stability and are susceptible to denaturation by temperature, pH, or other denaturing agent. Modification of FIX to increase stability can be accomplished while keeping activity unchanged compared to the unmodified or wild-type FIX. Alternatively, modification of FIX stability can be accomplished while increasing activity compared to the unmodified or wild-type FIX. Any methods known in the art can be used to create modified FIX polypeptides. In the methods described herein, modifications are chosen using the method of 2D-scanning mutagenesis as described, for example, in PCT published applications WO 2004/022747 and WO 2004/022593.

In principle, there are several general approaches described for protein-directed evolution based on mutagenesis. Any of these, alone or in combination can be used to modify a FIX polypeptide to achieve increased stability and/or resistance to proteolysis. Such methods include random mutagenesis, where the amino acids in the starting protein sequence are replaced by all (or a group) of the 20 amino acids either in single or multiple replacements at different amino acid positions are generated on the same molecule, at the same time. Another method, restricted random mutagenesis, introduces either all of the 20 amino acids or DNA-biased residues. The bias is based on the sequence of the DNA and not on that of the protein in a stochastic or semi-stochastic manner, respectively, within restricted or predefined regions of the protein known in advance to be involved in the activity being “evolved.” Additionally, methods of rational mutagenesis including 1D-scanning, 2D-scanning, and 3D-scanning can be used alone or in combination to construct modified FIX variants.

1. Non-Restricted Rational Mutagenesis One-Dimensional (1D)-Scanning

Rational mutagenesis, also termed 1D-scanning, is a two-step process, and is described in co-pending U.S. application Ser. No. 10/022,249 (U.S. Publication No. 2003/0134351-A1). 1D-scanning can be used to modify FIX polypeptides and, additionally, to identify positions for further modification by other methods such as 2D- and 3D-scanning. Briefly, in the first step, full-length amino acid scanning is performed where all and each amino acid in the starting FIX polypeptide sequence (for example SEQ ID NO: 2) is replaced by a designated reference amino acid (such as, alanine). Only a single amino acid is replaced on each protein molecule at a time. A collection of protein molecules having a single amino acid replacement is generated such that molecules differ from each other by the amino acid position at which the replacement has taken place. Mutant DNA molecules are designed, generated by mutagenesis and cloned individually, such as in addressable arrays, such that they are physically separated from each other and such that each one is the single product of an independent mutagenesis reaction. Mutant protein molecules derived from the collection of mutant nucleic acid molecules also are physically separated from each other, such as by formatting in addressable arrays. Activity assessment on each protein molecule allows for the identification of those amino acid positions that result in a drop in activity when replaced, thus indicating the involvement of that particular amino acid position in the protein's biological activity and/or conformation that leads to fitness of the particular feature being evolved. Those amino acid positions are referred to as HITs.

At the second step, a new collection of molecules is generated such that each molecule differs from each of the others by the amino acid present at the individual HIT positions identified in step 1. All 20 amino acids (19 remaining) are introduced at each of the HIT positions identified in step 1; while each individual molecule contains, in principle, one and only one amino acid replacement. Mutant DNA molecules are designed, generated by mutagenesis and cloned individually, such as in addressable arrays, such that they are physically separated from each other and such that each one is the single product of an independent mutagenesis reaction. Mutant protein molecules derived from the collection of mutant DNA molecules also are physically separated from each other, such as by formatting in addressable arrays. Activity assessment then is individually performed on each individual mutant molecule. The newly generated mutants that lead to a desired alteration (such as an improvement) in a protein activity are referred to as LEADs. This method permits an indirect search for property or activity alteration, such as improved stability and/or improved resistance to proteases or thermal conditions based on one rational amino acid replacement and sequence change at a single amino acid position at a time, in search of a new, unpredicted amino acid sequence at some unpredicted regions along a protein to produce a protein that exhibits a desired activity or altered activity, such as better performance than the starting protein.

In this approach, neither the amino acid position nor the replacing amino acid type are restricted. Full length protein scanning is performed during the first step to identify HIT positions, and then all 20 amino acids are tested at each of the HIT positions, to identify LEAD sequences; while, as a starting point, only one amino acid at a time is replaced on each molecule. The selection of the target region (HITs and surrounding amino acids) for the second step is based upon experimental data on activity obtained in the first step. Thus, no prior knowledge of protein structure and/or function is necessary. Using this approach, LEAD sequences have been found on proteins that are located at regions of the protein not previously known to be involved in the particular biological activity being modified; thus emphasizing the power of this approach to discover unpredictable regions (HITs) as targets for fitness improvement.

2. Two Dimensional (2D) Rational Scanning (Restricted Rational Mutagenesis)

The 2D-scanning (or restricted rational mutagenesis) methods for protein rational evolution (see, co-pending U.S. Published Application Nos. US 2005-0202438 A1 and US-2004-0132977-A1 and published International applications WO 2004/022593 and WO 2004/022747) are based on scanning over two dimensions. The first dimension is the amino acid position along the protein sequence, in order to identify is-HIT target positions. The second dimension is scanning the amino acid type selected for replacing a particular is-HIT amino acid position. An advantage of the 2D-scanning methods provided herein is that at least one, and typically the amino acid position and/or the replacing amino acid, can be restricted such that fewer than all amino acids on the protein-backbone are selected for amino acid replacement; and/or fewer than all of the remaining 19 amino acids available to replace an original, such as native, amino acid are selected for replacement.

In particular embodiments, based on i) the particular protein properties to be evolved (such as, resistance to proteolysis), ii) sequence of amino acids of the protein, and iii) the known properties of the individual amino acids, a number of target positions along the protein sequence are selected, in silico, as “is-HIT target positions.” This number of is-HIT target positions is as large as reasonably possible such that all reasonably possible target positions for the particular feature being evolved are included. In particular, embodiments where a restricted number of is-HIT target positions are selected for replacement, the amino acids selected to replace the is-HIT target positions on the particular protein being optimized can be either all of the remaining 19 amino acids or, more frequently, a more restricted group comprising selected amino acids that are contemplated to have the desired effect on protein activity. In another embodiment, so long as a restricted number of replacing amino acids are used, all of the amino acid positions along the protein backbone can be selected as is-HIT target positions for amino acid replacement. Mutagenesis then is performed by the replacement of single amino acid residues at specific is-HIT target positions on the protein backbone (such as, “one-by-one,” such as in addressable arrays), such that each individual mutant generated is the single product of each single mutagenesis reaction. Mutant DNA molecules are designed, generated by mutagenesis and cloned individually, such as in addressable arrays, such that they are physically separated from each other and that each one is the single product of an independent mutagenesis reaction. Mutant protein molecules derived from the collection of mutant DNA molecules also are physically separated from each other, such as by formatting in addressable arrays. Thus, a plurality of mutant protein molecules is produced. Each mutant protein contains a single amino acid replacement at only one of the is-HIT target positions. Activity assessment is then individually performed on each individual protein mutant molecule, following protein expression and measurement of the appropriate activity. An example of practice of this method is shown in the Examples in which mutant FIX molecules are produced.

The newly generated proteins that lead to altered, typically improved, target protein activity are referred to as LEADs. This method relies on an indirect search for protein improvement for a particular activity (such as increased resistance to proteolysis), based on amino acid replacement and sequence change at single or, in another embodiment, a limited number of amino acid positions at a time. As a result, optimized proteins, which have modified sequences of amino acids at some regions along the protein that perform better (at a particular target activity or other property) than or different from the starting protein, are identified and isolated.

2D-scanning on FIX was used to generate variants improved in protein stability, including improved resistance to proteolysis. To effect such modifications, amino acid positions were selected using in silico analysis of FIX.

a. Identifying in-Silico HITs

The 2D-scanning method for directed evolution of proteins includes identifying and selecting (using in silico analysis) specific amino acids and amino acid positions (referred to herein as is-HITs) along the protein sequence that are contemplated to be directly or indirectly involved in the feature being evolved. As noted, the 2D-scanning methods provided include the following two steps. The first step is an in silico search of a target sequence of amino acids of the protein to identify all possible amino acid positions that can be targets for the activity being evolved. This is effected, for example, by assessing the effect of amino acid residues on the property or properties to be altered on the protein, using any known standard software. The particulars of the in silico analysis is a function of the property to be modified.

Once identified, these amino acid positions or target sequences are referred to as “is-HITs” (in silico HITs). In silico HITs are defined as those amino acid positions (or target positions) that potentially are involved in the “evolving” feature, such as increased resistance to proteolysis. The discrimination of the is-HITs among all the amino acid positions in a protein sequence can be made based on the amino acid type at each position in addition to the information on the protein secondary or tertiary structure. In silico HITs constitute a collection of mutant molecules such that all possible amino acids, amino acid positions or target sequences potentially involved in the evolving feature are represented. No strong theoretical discrimination among amino acids or amino acid positions is made at this stage. In silico HIT positions are spread over the full length of the protein sequence. Single or a limited number of is-HIT amino acids are replaced at a time on the target FIX polypeptide.

A variety of parameters can be analyzed to determine whether or not a particular amino acid on a protein might be involved in the evolving feature, typically a limited number of initial premises (typically no more than 2) are used to determine the in silico HITs. For example, as described herein, to increase the stability of FIX, the first condition is the nature of the amino acids linked to stability of the molecule such as its participation in directing proteolytic cleavage. A second premise, for example, can be related to the specific position of those amino acids along the protein structure.

During the first step of identification of is-HITs according to the methods provided herein, each individual amino acid along the protein sequence is considered individually to assess whether it is a candidate for is-HIT. This search is done one-by-one and the decision on whether the amino acid is considered to be a candidate for a is-HIT is based on (1) the amino acid type; (2) the position in the protein and protein structure if known; and (3) the predicted interaction between that amino acid and its neighbors in sequence and space.

Is-HITs were identified for a number of properties of FIX that contribute to protein stability, such as removal/modification of protease sensitive sites. Such modifications contribute to protein stability and thereby, to increasing the half-life of a FIX polypeptide in vitro, in vivo or ex vivo.

b. Identifying Replacing Amino Acids

Once the is-HITs target positions are selected, the next step is identifying those amino acids that will replace the original, such as native, amino acid at each is-HIT position to alter the activity level for the particular feature being evolved. The set of replacing amino acids to be used to replace the original, such as native, amino acid at each is-HIT position can be different and specific for the particular is-HIT position. The choice of the replacing amino acids takes into account the need to preserve the physicochemical properties such as hydrophobicity, charge and polarity of essential (such as, catalytic, binding, etc.) residues and alter some other property of the protein (such as, protein stability). The number of replacing amino acids of the remaining 19 non-native (or non-original) amino acids that can be used to replace a particular is-HIT target position ranges from 1 up to about 19, and anywhere in between, depending on the properties for the particular modification.

Numerous methods of selecting replacing amino acids (also referred to herein as “replacement amino acids”) are well known in the art. Protein chemists determined that certain amino acid substitutions commonly occur in related proteins from different species. As the protein still functions with these substitutions, the substituted amino acids are compatible with protein structure and function. Often, these substitutions are to a chemically similar amino acid, but other types of changes, although relatively rare, also can occur.

Knowing the types of changes that are most and least common in a large number of proteins can assist with predicting alignments and amino acid substitutions for any set of protein sequences. Amino acid substitution matrices are used for this purpose. A number of matrices are available. A detailed presentation of such matrices can be found in the co-pending U.S. Published Application Nos. US 2005-0202438 A1 and US-2004-0132977-A1 and published International applications WO 2004/022593 and WO 2004/022747, each of which is incorporated herein in their entirety herein. Such matrices also are known and available in the art, for example in the reference listed below.

In amino acid substitution matrices, amino acids are listed horizontally and vertically, and each matrix position is filled with a score that reflects how often one amino acid would have been paired with the other in an alignment of related protein sequences. The probability of changing amino acid “A” into amino acid “B” is assumed to be identical to the reverse probability of changing “B” into “A”. This assumption is made because, for any two sequences, the ancestor amino acid in the phylogenetic tree is usually not known. Additionally, the likelihood of replacement should depend on the product of the frequency of occurrence of the two amino acids and on their chemical and physical similarities. A prediction of this model is that amino acid frequencies will not change over evolutionary time (Dayhoff et al., Atlas of Protein Sequence and Structure, 5(3): 345-352, 1978). Several exemplary amino acid substitution matrices, including, but not limited to block substitution matrix (BLOSUM) (Henikoff et al. (1992) Proc. Natl. Acad. Sci. USA, 89: 10915-10919), Jones et al. (1992) Comput. Appl. Biosci., 8: 275-282, Gonnet et al. (1992) Science, 256: 1433-1445, Fitch (1966) J. Mol. Evol., 16(1): 9-16, Feng et al. (1985) J. Mol. Evol., 21: 112-125, McLachlan (1971) J. Mol. Biol., 61: 409-424, Grantham (1974) Science, 185: 862-864, Miyata (1979) J. Mol. Evol., 12: 219-236, Rao (1987) J. Pept. Protein Res., 29: 276-281, Risler (1988) J. Mol. Biol., 204: 1019-1029, Johnson et al. (1993) J. Mol. Biol., 233: 716-738, and Point Accepted Mutation (PAM) (Dayhoff et al. (1978) Atlas of Protein Sequence and Structure 5: 345-352.

Dayhoff and coworkers developed a model of protein evolution that resulted in the development of a set of widely used replacement matrices (Dayhoff et al., (1978) Atlas of Protein Sequence and Structure 5(3):345-352) termed percent accepted mutation matrices (PAM). In deriving these matrices, each change in the current amino acid at a particular site is assumed to be independent of previous mutational events at that site. Thus, the probability of change of any amino acid A to amino acid B is the same, regardless of the previous changes at that site and also regardless of the position of amino acid A in a protein sequence.

In the Dayhoff approach, replacement rates are derived from alignments of protein sequences that are at least 85% identical; this constraint ensures that the likelihood of a particular mutation being the result of a set of successive mutations is low. Because these changes are observed in closely related proteins, they represent amino acid substitutions that do not significantly change the function of the protein. Hence, they are called “accepted mutations,” as defined as amino acid changes that are accepted by natural selection.

The outcome of the two steps set forth above, which is performed in silico is that: (1) the amino acid positions that are the target for mutagenesis are identified (referred to as is-HITs); and (2) the replacing amino acids for the original, such as native, amino acids at the is-HITs are identified, to provide a collection of candidate LEAD mutant molecules that are expected to perform differently from the native molecule. These are assayed for a desired optimized (or improved or altered) activity.

c. Construction of Modified Proteins and Biological Assays

Once is-HITs are selected as set forth above, replacing amino acids are introduced. Mutant proteins typically are prepared using recombinant DNA methods and assessed in appropriate biological assays for the particular activity (feature) optimized. An exemplary method of preparing the mutant proteins is by mutagenesis of the original, such as native, gene using methods well known in the art. Mutant molecules are generated one-by-one, such as in addressable arrays, such that each individual mutant generated is the single product of each single and independent mutagenesis reaction. Individual mutagenesis reactions are conducted separately, such as in addressable arrays where they are physically separated from each other. Once a population of sets of nucleic acid molecules encoding the respective mutant proteins is prepared, each is separately introduced one-by-one into appropriate cells for the production of the corresponding mutant proteins. This also can be performed, for example, in addressable arrays where each set of nucleic acid molecules encoding a respective mutant protein is introduced into cells confined to a discrete location, such as in a well of a multi-well microtiter plate. Each individual mutant protein is individually phenotypically characterized and performance is quantitatively assessed using assays appropriate for the feature being optimized (i.e., feature being evolved). Again, this step can be performed in addressable arrays. Those mutants displaying a desired increased or decreased performance compared to the original, such as native molecules are identified and designated LEADs. From the beginning of the process of generating the mutant DNA molecules up through the readout and analysis of the performance results, each candidate LEAD mutant is generated, produced and analyzed individually, such as from its own address in an addressable array. The process is amenable to automation.

3. Three Dimensional (3D) Scanning

3D scanning, as described in co-pending U.S. Published Application Nos. US 2005-0202438 A1 and US-2004-0132977-A1 and published PCT applications WO 2004/022747 and WO 2004/022593, is an additional method of rational evolution of proteins based on the identification of potential target sites for mutagenesis (is-HITs). The method uses comparison of patterns of protein backbone folding between structurally related proteins, irrespective of the underlying sequences of the compared proteins. Once the structurally related amino acid positions are identified on the protein of interest, then suitable amino acid replacement criteria, such as PAM analysis, can be employed to identify candidate LEADs for construction and screening.

For example, analysis of “structural homology” between and among a number of related vitamin K-dependent proteases can be used to identify on various members of the vitamin K-dependent protease family, those amino acid positions and residues that are structurally similar or structurally related. For example, 3D scanning can be used to identify amino acid positions on FIX that are structurally similar or structurally related to those found in factor VII mutants, for example, that have been modified for improved stability. Exemplary vitamin K-dependent proteases include, but are not limited to, prothrombin, factor VII, factor X and protein C.

Using the 3D-scanning methods described herein, once one protein within a family of proteins (such as, FIX within the vitamin-K dependent protease family) is modified using the methods provided herein for generating LEAD mutants, is-HITs can be identified for other or all proteins within a particular family by identifying the corresponding amino acid positions therein using structural homology analysis (based upon comparisons of the 3D structures of the family members with original protein to identify corresponding residues for replacement) as described hereinafter. The is-HITs for the family members identified in this manner then can be subjected to the next step of identifying replacing amino acids and further assayed to obtain LEADs or super-LEADs as described herein. Similarly, information from 2D-scanning performed on other vitamin K-dependent proteases such as prothrombin, factor VII, factor X or protein C, for example, can be used to optimize FIX polypeptides.

This method can be applied to any desired phenotype using any protein, such as a vitamin K-dependent protease, as the starting material to which an evolution procedure, such as the rational directed evolution procedure of U.S. Published Application No. US 2003-0134351 A1 or the 2-dimensional scanning method described herein. The structurally corresponding residues are then altered on members of the family to produce additional vitamin K-dependent proteases with similar phenotypic alterations.

a. Homology

Typically, homology between proteins is compared at the level of their amino acid sequences, based on the percent or level of coincidence of individual amino acids, amino acid per amino acid, when sequences are aligned starting from a reference, generally the residue encoded by the start codon. For example, two proteins are said to be “homologous” or to bear some degree of homology whenever their respective amino acid sequences show a certain degree of matching upon alignment comparison. Comparative molecular biology is primarily based on this approach. From the degree of homology or coincidence between amino acid sequences, conclusions can be made on the evolutionary distance between or among two or more protein sequences and biological systems.

The concept of “convergent evolution” is applied to describe the phenomena by which phylogenetically-unrelated organisms or biological systems have evolved to share features related to their anatomy, physiology and structure as a response to common forces, constraints and evolutionary demands from the surrounding environment and living organisms. Alternatively, “divergent evolution,” is applied to describe the phenomena by which strongly phylogenetically related organisms or biological systems have evolved to diverge from identity or similarity as a response to divergent forces, constraints and evolutionary demands from the surrounding environment and living organisms.

In the typical traditional analysis of homologous proteins there are two conceptual biases corresponding to: i) “convergent evolution,” and ii) “divergent evolution.” Whenever the aligned amino acid sequences of two proteins do not match well with each other, these proteins are considered “not related” or “less related” with each other and have different phylogenetic origins. There is no (or low) homology between these proteins and their respective genes are not homologous (or show little homology). If these two “non-homologous” proteins under study share some common functional features (such as, interaction with other specific molecules, activity), they are determined to have arisen by “convergent evolution,” i.e., by evolution of their non-homologous amino acid sequences, in such a way that they end up generating functionally “related” structures.

On the other hand, whenever the aligned amino acid sequences of two proteins do match with each other to a certain degree, these proteins are considered to be “related” and to share a common phylogenetic origin. A given degree of homology is assigned between these two proteins and their respective genes likewise share a corresponding degree of homology. During the evolution of their initial highly homologous amino acid sequence, enough changes can be accumulated in such a way that they end up generating “less-related” sequences and less related function. The divergence from perfect matching between these two “homologous” proteins under study is said come from “divergent evolution.”

b. 3D-Scanning (Structural Homology) Methods

Structural homology refers to homology between the topology and three-dimensional structure of two proteins. Structural homology is not necessarily related to “convergent evolution” or to “divergent evolution,” nor is it related to the underlying amino acid sequence. Rather, structural homology is likely driven (through natural evolution) by the need of a protein to fit specific conformational demands imposed by its environment. Particular structurally homologous “spots” or “loci” would not be allowed to structurally diverge from the original structure, even when its own underlying sequence does diverge. This structural homology is exploited herein to identify loci for mutation.

Within the amino acid sequence of a protein resides the appropriate biochemical and structural signals to achieve a specific spatial folding in either an independent or a chaperon-assisted manner. Indeed, this specific spatial folding ultimately determines protein traits and activity. Proteins interact with other proteins and molecules in general through their specific topologies and spatial conformations. In principle, these interactions are not based solely on the precise amino acid sequence underlying the involved topology or conformation. If protein traits, activity (behavior and phenotypes) and interactions rely on protein topology and conformation, then evolutionary forces and constraints acting on proteins can be expected to act on topology and conformation. Proteins sharing similar functions will share comparable characteristics in their topology and conformation, despite the underlying amino acid sequences that create those topologies and conformations.

4. Super-LEADs and Additive Directional Mutagenesis (ADM)

Modification of FIX polypeptides also can include combining two or more mutations. For example, Additive Directional Mutagenesis (ADM) can be used to assemble on a single mutant protein multiple mutations present on the individual LEAD molecules, so as to generate super-LEAD mutant proteins (see co-pending U.S. Published Application Nos. US 2005-0202438 A1 and US-2004-0132977-A1 and published PCT applications WO 2004/022747 and WO 2004/022593). ADM is a repetitive multi-step process where at each step after the creation of the first LEAD mutant protein a new LEAD mutation is added onto the previous LEAD mutant protein to create successive super-LEAD mutant proteins. ADM is not based on genetic recombination mechanisms, nor on shuffling methodologies; instead it is a simple one-mutation-at-a-time process, repeated as many times as necessary until the total number of desired mutations is introduced on the same molecule. To avoid the exponentially increasing number of all possible combinations that can be generated by putting together on the same molecule a given number of single mutations, a method is provided herein that, although it does not cover all the combinatorial possible space, still captures a big part of the combinatorial potential. “Combinatorial” is used herein in its mathematical meaning (i.e., subsets of a group of elements, containing some of the elements in any possible order) and not in the molecular biological or directed evolution meaning (i.e., generating pools, or mixtures, or collections of molecules by randomly mixing their constitutive elements).

A population of sets of nucleic acid molecules encoding a collection of new super-LEAD mutant molecules is generated tested and phenotypically characterized one-by-one in addressable arrays. Super-LEAD mutant molecules are such that each molecule contains a variable number and type of LEAD mutations. Those molecules displaying further improved fitness for the particular feature being evolved are referred to as super-LEADs. Super-LEADs can be generated by other methods known to those of skill in the art and tested by the high throughput methods herein. For purposes herein a super-LEAD typically has activity with respect to the function or biological activity of interest that differs from the improved activity of a LEAD by a desired amount, such as at least about or 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200%, 300%, 400%, 500%, or more from at least one of the LEAD mutants from which it is derived. In yet other embodiments, the change in activity is at least about 2 times, 3 times, 4 times, 5 times, 6 times, 7 times, 8 times, 9 times, 10 times, 20 times, 30 times, 40 times, 50 times, 60 times, 70 times, 80 times, 90 times, 100 times, 200 times, 300 times, 400 times, 500 times, 600 times, 700 times, 800 times, 900 times, 1000 times, or more greater than at least one of the LEAD molecules from which it is derived. As with LEADs, the change in the activity for super-LEADs is dependent upon the property that is being “evolved.” The desired alteration, which can be either an increase or a reduction in a feature or property, will depend upon the function or property of interest.

In one embodiment, the ADM method employs a number of repetitive steps, such that at each step a new mutation is added on a given molecule. Although numerous different ways are possible for combining each LEAD mutation onto a super-LEAD protein, an exemplary way the new mutations (such as, mutation 1 (m1), mutation 2 (m2), mutation 3 (m3), mutation 4 (m4), mutation 5 (m5), mutation n (mn)) can be added corresponds to the following diagram:

m1

m1+m2

m1+m2+m3

m1+m2+m3+m4

m1+m2+m3+m4+m5

m1+m2+m3+m4+m5+ . . . +nm

m1+m2+m4

m1+m2+m4+m5

m1+m2+m4+m5+ . . . +nm

m1+m2+m5

m1+m2+m5+ . . . +nm

m2

m2+m3

m2+m3+m4

m2+m3+m4+m5

m2+m3+m4+m5+ . . . +nm

m2+m4

m2+m4+m5

m2+m4+m5+ . . . +nm

m2+m5

m2+m5+ . . . +nm

. . . , etc. . . .

5. Multi-Overlapped Primer Extensions

Another method that can be employed to generate combinations of two or more mutations is using oligonucleotide-mediated mutagenesis referred to as “multi overlapped primer extensions”. This method can be used for the rational combination of mutant LEADs to form super-LEADS. This method allows the simultaneous introduction of several mutations throughout a small protein or protein-region of known sequence. Overlapping oligonucleotides of typically around 70 bases in length (since longer oligonucleotides lead to increased error) are designed from the DNA sequence (gene) encoding the mutant LEAD proteins in such a way that they overlap with each other on a region of typically around 20 bases. Although typically about 70 bases are used to create the overlapping oligonucleotides, the length of additional overlapping oligonucleotides for use can range from about 30 bases up to about 100 bases. Likewise, although typically the overlapping region of the overlapping oligonucleotides is about 20 bases, the length of other overlapping regions for use herein can range from about 5 bases up to about 40 bases. These overlapping oligonucleotides (including or not point mutations) act as template and primers in a first step of PCR (using a proofreading polymerase, such as, Pfu DNA polymerase, to avoid unexpected mutations) to create small amounts of full-length gene. The full-length gene resulting from the first PCR is then selectively amplified in a second step of PCR using flanking primers, each one tagged with a restriction site in order to facilitate subsequent cloning. One multi overlapped extension process yields a full-length (multi-mutated) nucleic acid molecule encoding a candidate super-LEAD protein having multiple mutations therein derived from LEAD mutant proteins.

E. MODIFIED FIX POLYPEPTIDES EXHIBITING INCREASED PROTEIN STABILITY, PARTICULARLY MODIFICATIONS THAT INCREASE RESISTANCE TO PROTEASES

Provided herein are modified FIX polypeptides (also referred to herein as variants of FIX) that display improved protein stability (i.e. increased protease resistance, or increased conformational stability that, for example, renders a polypeptide more resistant to denaturation by temperature or pH changes). A FIX polypeptide provided herein exhibiting increased protein stability can lead to an increased half-life of the polypeptide in vitro (such as, during production, purification and storage) or in vivo (such as, after administration to a subject). For example, increased half-life can occur following administration of the polypeptide to a subject, such as a human subject. The increased half-life of the modified FIX polypeptide can be increased by an amount that is at least about or 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200%, 300%, 400%, 500%, or more compared to the half-life of the unmodified FIX polypeptide. In some examples, the increased half-life of the modified FIX polypeptide can be increased by an amount that is at least 6 times, 7 times, 8 times, 9 times, 10 times, 20 times, 30 times, 40 times, 50 times, 60 times, 70 times, 80 times, 90 times, 100 times, 200 times, 300 times, 400 times, 500 times, 600 times, 700 times, 800 times, 900 times, 1000 times, or more times when compared to the half-life of the unmodified FIX polypeptide. Hence, the modified FIX polypeptides provided herein offer FIX with advantages including a decrease in the frequency of injections needed to maintain a sufficient drug level in serum, thus leading to, for example, higher comfort and acceptance by subjects, lower doses necessary to achieve comparable biological effects and attenuation of secondary effects.

Provided herein are modified FIX polypeptides containing modifications that alter any one or more of the properties of FIX that contribute to increased protein stability, such as increased protease resistance, and any combinations of the modifications thereof. Increased protein stability can be accomplished by amino acid replacement, such that resistance to proteases by amino acid replacements can be achieved by direct destruction of the protease target residue or sequence. Generally, modified FIX polypeptides retain one or more activities of an unmodified FIX polypeptide. For example, the modified FIX polypeptides provided herein exhibit at least one activity that is substantially unchanged (less than 1%, 5% or 10% changed) compared to the unmodified or wild-type FIX. In other examples, the activity of a modified FIX polypeptide is increased or is decreased as compared to an unmodified FIX polypeptide. In another embodiment, the modified FIX polypeptides provided herein can inhibit an activity of the unmodified and/or wild-type native FIX polypeptide. Activity includes, for example, but not limited to blood coagulation, platelet binding, cofactor binding and protease activity. Activity can be assessed in vitro or in vivo and can be compared to the unmodified FIX polypeptide, such as for example, the mature, wild-type native FIX polypeptide (SEQ ID NO: 2), the wild-type precursor FIX polypeptide (SEQ ID NO: 1), or any other FIX polypeptide known to one of skill in the art that is used as the starting material.

Modified FIX polypeptides provided herein can be modified at one or more amino acid positions corresponding to amino acid positions of a mature FIX polypeptide, for example, a mature FIX polypeptide having an amino acid sequence set forth in SEQ ID NO: 2. FIX polypeptides can be modified compared to a mature or precursor FIX polypeptide having an amino acid sequence set forth in SEQ ID NO: 2 or 1, respectively. Modified FIX polypeptides provided herein include human FIX (hFIX) variants. An exemplary hFIX variant occurs at amino acid position 148 of the mature hFIX polypeptide, wherein the amino acid is Alanine or Threonine. The hFIX polypeptide can be of any human tissue or cell-type origin. Modified FIX polypeptides provided herein also include variants of FIX of non-human origin. Such alignments and selection of positions can be performed with any FIX polypeptide by aligning it with hFIX and selecting corresponding positions for modification. For example, modified FIX polypeptides can be variants of a non-human FIX, including, but not limited to, mouse, rat, guinea pig, cow, sheep, dog, cat, chicken, pig, rabbit, fish, and chimpanzee FIX. Exemplary unmodified non-human FIX polypeptides have amino acid sequences set forth in SEQ ID NOS: 898-912. Modified FIX polypeptides also include polypeptides that are hybrids of different FIX polypeptides and also synthetic FIX polypeptides prepared recombinantly or synthesized or constructed by other methods known in the art based upon known polypeptides.

Typically, modifications include replacement (substitution), addition, deletion or a combination thereof, of amino acid residues as described herein. Modified FIX polypeptides include those with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more modified positions. Generally, the modification results in increased stability without losing at least one activity, such as coagulant activity (L e. retains at least one activity as defined herein) of an unmodified FIX polypeptide. A modified FIX exhibiting increased protein stability containing a single amino acid change at an is-HIT position as compared to an unmodified FIX is called a LEAD. FIX polypeptide candidate LEAD polypeptides can include amino acid replacement or replacements at any one or more of the is-HIT positions selected using methods described herein or known in the art, such as obtained using PAM analysis. Exemplary amino acid modifications corresponding to amino acid positions of a mature FIX polypeptide that can contribute to an increase in protein stability with respect to protease resistance are set forth in Table 5. In Table 5 below, the sequence identifier (SEQ ID NO.) is in parenthesis next to each substitution.

Also among the variants provided herein are modified FIX polypeptides with two or more modifications compared to native or wild-type FIX. Modified FIX polypeptides include those with 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more modified positions. The two or more modifications can include two or more modifications of the same property, such as, two modifications that modify resistance to proteases (blood, intestinal, etc.). In another embodiment, the two or more modifications include combinations of properties that each contribute to FIX stability. For example, a FIX variant can include one or more modifications that remove a protease sensitive site and one or more modifications that alter FIX conformational stability. FIX variants carrying replacements at more than one is-HIT sites and displaying improved stability are called super-LEADs. A FIX super-LEAD can for example, contain 2, 3, 4, 5, 6, 7, 8, 9, 10 or more than 10 amino acid changes compared to wild-type or unmodified FIX. In one example, a modified FIX polypeptide candidate super-LEAD can contain two or more amino acid modifications set forth in Table 5.

1. Protease Resistance

The delivery of stable peptide and protein drugs to patients is a major challenge for the pharmaceutical industry. These types of drugs in the human body are constantly eliminated or taken out of circulation by different physiological processes including internalization, glomerular filtration and proteolysis. The latter is often the limiting process affecting the half-life of proteins used as therapeutic agents in per-oral administration and either intravenous or intramuscular injections. To solve this problem, therapeutic proteins that increase protein stability manifested as an increased resistance to digestion by proteases are provided. Among modifications for therapeutic proteins are those that increase protection against protease digestion without destroying or completely eliminating a therapeutic use or the therapeutic activity. Such changes result in longer-lasting therapeutic proteins, and, also permit oral administration of therapeutic proteins.

FIX polypeptides provided herein are modified to increase resistance to proteolysis compared to in the absence of the modification. The resulting FIX polypeptides exhibit increased the half-life of the modified FIX polypeptide in vitro (such as, for production, processing, storage and assays.) and/or in vivo (such as, serum stability) and/or other properties, such as increased bioavailability upon oral administration. The modifications that alter susceptibility to cleavage by a proteases, unless specifically desired, do not alter activation cleavage sites for conversion of the zymogen into an activated form.

Proteases, proteinases or peptidases catalyze the hydrolysis of covalent peptidic bonds. Modified FIX polypeptides provided herein exhibit increased resistance to proteolysis by proteases, including those that occur, for example, in body fluids and tissues, such as those that include, but are not limited to, saliva, blood, serum, intestinal, stomach, blood, cell lysates, cells and others. These include proteases of all types, such as, for example, serine proteases and matrix metalloproteinases.

Modifications of FIX polypeptides result in resistance to one or more proteases that include, but are not limited to, pepsin, trypsin, chymotrypsin, elastase, aminopeptidase, gelatinase B, gelatinase A, α-chymotrypsin, carboxypeptidase, endoproteinase Arg-C, endoproteinase Asp-N, endoproteinase Glu-C, endoproteinase Lys-C, luminal pepsin, microvillar endopeptidase, dipeptidyl peptidase, enteropeptidase, hydrolase, NS3, factor Xa, Granzyme B, thrombin, plasmin, urokinase, tPA and PSA.

FIX polypeptides are cleaved by proteases and their activity reduced or inactivated. For example, human neutrophil elastase cleaves and inactivate FIX polypeptides after amino acid residues, such as T140, T144, I164, T172, and V181 (see, e.g., Takaki et al. (1983) J. Clin. Invest. 72: 1706-1715 and Samis et al. (1998) Blood 92(4): 1287-1296). In another example, thrombin cleaves and inactivates FIX polypeptides after amino acid residues, such as R318 and R327 (see, e.g., Kisiel et al. Blood 66(6): 1302-1308 (1985). Plasmin cleaves and inactivates FIX polypeptides after amino acid residues (Samis et al. (2000) Blood 95(3) 943-951). As shown herein, modifications of FIX polypeptides at sites, such as such as K43, R145, R180, K316, and R318 increase resistance of the FIX polypeptides to hydrolysis a protease. In a non-limiting example, modification of T140, T144, I164, T172 and/or V181 or other sites of a mature FIX polypeptide is shown herein to increase resistance to elastase.

Modified FIX polypeptides provided herein exhibit increased resistance to proteolysis, particularly by enzymes present in serum, blood, the gut, the mouth and other body fluids. Such increase in resistance can manifested as increased half-life of the FIX polypeptide by an amount that is at least about or 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200%, 300%, 400%, 500%, or more compared to the unmodified or wild-type FIX polypeptide in either in vivo (such as in human blood, human serum, saliva, digestive fluid and the intestinal tract,) and/or an in vitro mixture containing one or more proteases. Increased resistance also is manifested by increased bioavailability upon oral administration. As described herein, therapeutic proteins are not generally amenable to oral administration by virtue of the activity of digestive and/or blood and serum proteases. The modified FIX polypeptides provided herein can be administered orally. Hence, as described herein, provided are oral compositions containing a modified FIX polypeptide. The oral compositions do not require additional protease inhibitors nor any additional modifications of the FIX polypeptides. Additional modifications of the FIX polypeptides are optional.

Typically, the half-life in vitro or in vivo of the modified FIX polypeptides provided herein is increased by an amount selected from at least about or 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200%, 300%, 400%, 500%, or more when compared to the half-life of unmodified or wild-type FIX in either blood, serum, or in an in vitro preparation or an in vitro mixture containing one or more proteases.

Typically, the modified FIX polypeptides provided herein exhibit at least one activity that is substantially unchanged (less than 1%, 5% or 10% changed) compared to the unmodified or wild-type FIX. In some examples, the activity is increased compared to the unmodified FIX. In other examples, the activity is decreased compared to the unmodified FIX polypeptide. The activity is retained at level so that the FIX polypeptide can be used therapeutically for the desired purpose. Activity includes, for example, blood coagulation activity, and can be compared to the unmodified polypeptide, such as for example, the mature, wild-type native FIX polypeptide (SEQ ID NO: 2), the wild-type precursor FIX polypeptide (SEQ ID NO: 1), or any other FIX polypeptide used as the starting material. In another embodiment the modified FIX polypeptide can inhibit one or more activities of an unmodified FIX polypeptide and/or act as an anticoagulant.

The FIX polypeptides can be modified to have resistance to a variety of proteases. These include, for example, members of the serine protease family and also metalloproteinases.

a. Serine Proteases

Serine proteases participate in a range of functions in the body, including blood clotting, inflammation as well as digestive enzymes in prokaryotes and eukaryotes. Serine proteases are sequence specific. While cascades of protease activations control blood clotting and complement, other proteases are involved in signaling pathways, enzyme activation and degradative functions in different cellular or extracellular compartments.

Serine proteases include, but are not limited, to chymotrypsin, trypsin, elastase, NS3, factor Xa, Granzyme B, thrombin, plasmin, urokinase, tPA and PSA. Chymotrypsin, trypsin and elastase are synthesized by the pancreatic acinar cells, secreted in the small intestine and are responsible for catalyzing the hydrolysis of peptide bonds. All three of these enzymes are similar in structure, as shown through their X-ray structures. Each of these digestive serine proteases targets different regions of the polypeptide chain, based upon the amino acid residues and side chains surrounding the site of cleavage. The active site of serine proteases is shaped as a cleft where the polypeptide substrate binds. Amino acid residues are labeled from N to C term of the polypeptide substrate (Pi, . . . , P3, P2, P1, P1′, P2′, P3′, . . . , Pj) and their respective binding sub-sites (Si, . . . , S3, S2, S1, S1′, S2′, S3′, . . . , Sj). The cleavage is catalyzed between P1 and P1′. Chymotrypsin hydrolyzes peptide bonds flanked with bulky hydrophobic amino acid residues. Particular residues include phenylalanine, tryptophan and tyrosine, which fit into a snug hydrophobic pocket. Trypsin hydrolyzes peptide bonds flanked with positively charged amino acid residues. Instead of having the hydrophobic pocket of the chymotrypsin, trypsin possesses an aspartic acid residue at the back of the pocket, which can interact with positively charged residues such as arginine and lysine. Elastase hydrolyzes peptide bonds flanked with small neutral amino acid residues, such as alanine, glycine and valine. In contrast to trypsin and chymotrypsin, elastase contains a pocket that is lined with valine and threonine, rendering it a mere depression, which can accommodate the smaller amino acid residues. Serine proteases are ubiquitous in prokaryotes and eukaryotes and serve important and diverse biological functions such as hemostasis, fibrinolysis, complement formation and the digestion of dietary proteins. Coagulation factors, such as FIX, FVII and FX possess serine protease domains that hydrolyze specific members of the coagulation cascade.

Elastases that belong to the serine protease family display extensive sequence homology to other known serine proteases, including trypsin and chymotrypsin. Serine elastases preferentially cleave polypeptides adjacent to aliphatic amino acids residues, typically alanine, valine and methionine, and to a lesser extent, leucine and isoleucine. Humans have six elastase genes which encode the structurally similar proteins, elastase 1 (ELA-1, also known as pancreatic elastase, PE), elastase 2 (neutrophil elastase, NE, also known as PMN elastase, bone marrow serine protease, medullasin, human leukocyte elastase, HLE), elastase 2A (ELA-2A), elastase 2B (ELA-2B), elastase 3A (ELA-3A, elastase IIIA, Protease E), and elastase-3B (ELA-3B, elastase IIIB, protease E). Other serine proteases with elastase activity include, but are not limited to, proteinase-3 (PR-3), endogenous vascular elastase (EVE), and endothelial cell elastase (ECE).

Neutrophil primary azurophil granules carry NE (ELA-2) and PR-3, which are released upon neutrophil activation. NE is involved in degradation of the extracellular matrix and (ECM), including degradation of elastin, cartilage proteoglycans, collagens, and fibronectin, and digestion of material taken into the cell by phagocytosis. NE also helps in degradation of proteins, such as immunoglobulins and surfactant apoproteins. NE preferentially cleaves Val-X bonds and to a lesser extent Ala-X bonds. Abnormal or excessive release of NE has been linked to defects in connective tissue turnover, arthritis and inflammation. Like NE, PR-3 also functions to activate proenzymes, such as metalloproteinases, and cytokines, such as TNF-α, IL-1β, and interleukin-8 (IL-8).

Pancreatic elastase (ELA-1) preferentially cleaves Ala-X bonds and is expressed primarily in skin keratinocytes. Expression of ELA is not normally found in the adult pancreas though it is often expressed in and used as a marker for pancreatic cancers. Elastase activity of the normal pancreas is attributable to ELA-2A and ELA-2B. ELA-2A and ELA-2B preferentially cleaves Leu-X, Met-X and Phe-X bonds.

Some pathological conditions are result at least in part from an imbalance between the elastases and their endogenous inhibitors. Uncontrolled proteolytic degradation by neutrophil elastases, especially ELA-2 has been implicated in a number of pathological conditions like pulmonary emphysema, acute respiratory distress syndrome, septic shock, multiple organ failure, rheumatoid arthritis and cystic fibrosis.

High concentrations of elastases can be found in the gastrointestinal tract and blood stream. Hence, effective therapeutics to be administered via these routes can be achieved through modification of elastase cleavage sites. As mentioned above, FIX is known to be cleaved by human neutrophil elastase (HNE) at amino acid positions T140, T144, I164, T172 and V181 of a mature FIX polypeptide. Cleavage of FIX by HNE generates a FIX polypeptide without coagulant activity. Modification of FIX polypeptides at one or more elastase cleavage sites can increase resistance of FIX polypeptides to proteolytic degradation and thus, improve the therapeutic properties of the FIX polypeptide.

Increased levels of elastase are associated with coagulation disease states, such as disseminated intravascular coagulation (DIC), wherein there is a depletion of active coagulation factors. The decrease in pool of coagulation factors can result in excessive bleeding at sites of tissue damage due to the deficiency in clotting factors needed at the injury location. Modification of FIX polypeptides at elastase cleavage sites, such as the modified FIX polypeptides provided herein, can increase the resistance of FIX polypeptides to elevated levels of elastase in such disease states and thus, improve the therapeutic effectiveness of FIX polypeptides.

b. Matrix Metalloproteinases

Matrix metalloproteinases (MMPs) are a family of Zn²⁺- and calcium-dependent endopeptidases that degrade components of the extracellular matrix (ECM). In addition, MMPs also can process a number of cell-surface cytokines, receptors and other soluble proteins. They are involved in normal tissue remodeling processes such as wound healing, pregnancy and angiogenesis. Under physiological conditions, MMPs are made as inactive precursors (zymogens) and are processed to their active form. Additionally, the enzymes are specifically regulated by endogenous inhibitors called tissue inhibitors of matrix metalloproteinases (TIMPs). The proteolytic activity of MMPs acts as an effector mechanism of tissue remodeling in physiologic and pathologic conditions, and as modulator of inflammation. The excess synthesis and production of these proteins lead to accelerated degradation of the ECM which is associated with a variety of diseases and conditions such as, for example, bone homeostasis, arthritis, cancer, multiple sclerosis and rheumatoid arthritis. In the context of neuroinflammatory diseases, MMPs have been implicated in processes such as (a) blood-brain barrier (BBB) and blood-nerve barrier opening, (b) invasion of neural tissue by blood-derived immune cells, (c) shedding of cytokines and cytokine receptors, and (d) direct cellular damage in diseases of the peripheral and central nervous system (Leppert et al. (2001) Brain Res. Rev. 36(2-3): 249-57; Borkakoti et al. (1998) Prog. Biophys. Mol. Biol. 70(1): 73-94).

Members of the MMP family include collagenases, gelatinases, stromelysins, matrilysin and membrane-bound MMPs. Most MMPs are secreted in the inactive proenzyme form. The secreted proenzyme MMPs can be activated by several proinflammatory agents such as oxidants, proteinases including elastase, plasmin, and trypsin, and other MMPs (Cuzner and Opdenakker (1999) J. Neuroimmunol. 94(1-2): 1-14). In tissues, physiological MMP activators include tissue or plasma proteinases or opportunistic bacterial proteinases. For example, the plasminogen activator/plasmin system, including ubiquitous plasminogen by urokinase (u-Pa) and tissue-type plasminogen activator (t-Pa), is an important activator of pro-MMP in pathological situations. MMP activity can be inhibited by tissue inhibitors of metalloproteinases (TIMPs), by serine proteinase inhibitors (serpins), and by nonspecific proteinase inhibitors, such as α2-macroglobulin. TIMPs inhibit the MMP activity through noncovalent binding of the active zinc-binding sites of MMPs. Proteolytic activities of MMPs and plasminogen activators, and their inhibitors, are important in maintaining the integrity of the ECM as cell-ECM interactions influence and mediate a wide range of processes including proliferation, differentiation, adhesion and migration of a variety of cell types. Excessive production of matrix metalloproteinases has been implicated in tissue damage and wound healing, inflammatory disorders, proliferative disorders and autoimmune diseases (St-Pierre et al. (2003) Curr. Drug Targets Inflamm. Allergy 2(3): 206-215; Opdenakker (1997) G. Verh. K. Acad. Geneeskd. Belg. 59(6): 489-514).

c. Increased Resistance to Proteolysis by Removal of Proteolytic Sites

As exemplified herein, the 2D-scanning methodology was used to identify the amino acids of hFIX that lead to an increase in stability when challenged with proteases (such as blood and/or intestinal proteins), blood lysate and/or serum. Increasing protein stability to proteases (such as blood, lysate and intestinal serum), provides a longer in vivo half-life for the particular protein molecules. This can reduce the frequency of administered doses and/or the total amount administered.

A first step in the design of hFIX mutants provided resistant to proteolysis included identifying sites vulnerable to proteolysis along the protein sequence. Based on a list of selected blood, intestinal or any other type of proteases considered (Table 4), the complete list of all amino acids and sequences of amino acids in hFIX that can be targeted by those proteases was first determined in silico. The protease targets (amino acids or sequences of amino acids along the hFIX polypeptide) are named in silico HITs (is-HITs).

The second step in the design of hFIX mutants that are resistant to proteolysis included identifying the appropriate replacing amino acids such that if they replaced the natural amino acids in hFIX at is-HITs, the protein (i) becomes resistant to proteolysis; and (ii) elicits a level of activity at least comparable to the wild-type hFIX polypeptide. In another embodiment the protein (i) becomes resistant to proteolysis; and (ii) inhibits an activity of the wild-type hFIX polypeptide and/or acts as an anticoagulant. The choice of the replacing amino acids included consideration of the broad target specificity of certain proteases and the need to preserve the physicochemical properties such as hydrophobicity, charge and polarity of essential (such as, catalytic, binding, etc.) residues in hFIX.

“Point Accepted Mutation” (PAM; Dayhoff et al., 1978) can be used as part of the 2D scanning approach. PAM values, originally developed to produce alignments between protein sequences, are available in the form of probability matrices that reflect an evolutionary distance between amino acids. Conservative substitutions of a residue in a reference sequence are those substitutions that are physically and functionally similar to the corresponding reference residues, i.e., that have a similar size, shape, electric charge, and/or chemical properties, including the ability to form covalent or hydrogen bonds and other such interactions. Conservative substitutions show the highest scores fitting with the PAM matrix criteria in the form of accepted point mutations. The PAM250 matrix is used in the frame of 2D-scanning to identify candidate replacing amino acids for the is-HITs in order to generate conservative mutations without affecting protein function. At least two amino acids with the highest values in PAM250 matrix corresponding to conservative substitutions or accepted point mutations were chosen for replacement at each is-HIT. The replacement of amino acids by cysteine residues is explicitly avoided since this change can lead to the formation of intermolecular disulfide bonds.

Briefly, using the algorithm PROTEOL (on-line at infobiogen.fr and at bioinfo.hku.hk/services/analyseq/cgi-bin/proteol_in.pl), a list of residues along the mature hFIX polypeptide of 415 amino acids (SEQ ID NO: 2), which can be recognized as substrate for proteases (blood, intestinal, etc.) in Table 4 was established. The algorithm generates a proteolytic digestion map based on a list of proteases, the proteolytic specificity of the proteases, and the polypeptide amino acid sequence that is entered. Table 4 shows the in silico identification of amino acid positions that are targets for proteolysis using selected proteases and chemical treatment.

TABLE 4 Amino Acid Protease or Chemical Abbreviation Position Treatment AspN D Endoproteinase Asp-N Chymo (F, W, Y, M, L)~P Chymotrypsin Clos R Clostripain CnBr M Cyanogen Bromide IBzO W IodosoBenzoate Myxo K Myxobacter NH₂OH N G Hydroxylamine pH2.5 D P pH 2.5 ProEn P Proline Endopeptidase Staph E Staphylococcal Protease Tryp (K, R)~P Trypsin TrypK K~P Trypsin (Arg blocked) TrypR R~P Trypsin (Lys blocked)

Is-HITS were identified and LEADS created for higher resistance to proteolysis of hFIX. The native amino acids at each of the is-HIT positions and replacing amino acids for increased resistance to proteolysis can include, but are not limited to replacing any of Y, A, L, S, T, I, V, F, Q and M by any of E, D, K, R, N, Q, S and T. Is-HITS and LEADs can include modifications at regions susceptible to proteolysis.

d. Modified FIX Polypeptides Exhibiting Increased Protease Resistance

Using such methods as outlined above, modified FIX proteins were generated. Sites, designated is-HIT positions, were identified and modified proteins prepared. The resulting proteins exhibited increased protease resistance. This was manifested as, for example, increased the methods described herein, the following is-HIT positions were identified to eliminate protease sensitive sites and increase protein stability of a FIX polypeptide. In addition, the modified FIX proteins can be administered orally and deliver therapeutically effective dosages to the blood.

Among the modified FIX polypeptides provided herein are those that included modifications at one or more loci. Typically modified FIX polypeptides include one, two, three, four or five such modifications. In addition, the background polypeptide that is modified can include other modifications known to alter desired properties, such as modification of sites to decrease immunogenicity and/or to increase glycosylation. The polypeptides can include further modifications, such as pegylation.

Provided herein are modified FIX polypeptides that include modifications of the amino acids at positions selected from among one or more of the following: 1, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 52, 53, 55, 57, 58, 59, 60, 61, 63, 64, 65, 66, 68, 69, 70, 72, 74, 75, 76, 77, 78, 79, 80, 82, 83, 84, 85, 86, 87, 90, 91, 92, 93, 94, 96, 98, 100, 101, 102, 103, 104, 106, 107, 108, 110, 112, 113, 114, 115, 116, 117, 118, 119, 122, 123, 125, 126, 127, 128, 129, 131, 133, 134, 135, 136, 137, 138, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 151, 152, 153, 154, 155, 156, 158, 159, 160, 161, 162, 163, 164, 165, 166, 168, 169, 171, 172, 174, 175, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 192, 193, 194, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 207, 208, 209, 210, 211, 213, 214, 215, 216, 217, 218, 219, 220, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 238, 239, 240, 241, 242, 244, 245, 247, 248, 250, 251, 252, 253, 254, 255, 259, 261, 262, 263, 265, 266, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 283, 284, 285, 286, 287, 288, 290, 291, 292, 293, 294, 295, 296, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 316, 317, 318, 319, 320, 321, 322, 323, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 337, 338, 339, 340, 341, 342, 343, 344, 345, 348, 349, 351, 352, 353, 355, 356, 357, 358, 359, 360, 363, 364, 365, 366, 367, 368, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 407, 408, 409, 410, 411, 412, 413, 414, and 415. These positions (loci) are relative to the mature FIX polypeptide whose sequence is set forth in SEQ ID NO.: 2 or 1035 or corresponding loci in an allelic or species variant and/or in a background polypeptide (starting FIX polypeptide) including other modifications. The FIX polypeptides include precursor forms and mature forms, zymogens and activated forms.

In particular examples, amino acid replacement or replacements can be at any one or more positions corresponding to any of the following positions: Y1, S3, G4, K5, L6, E7, E8, F9, V10, G12, L14, E15, R16, E17, M19, E20, E21, K22, S24, F25, E26, E27, A28, R29, E30, V31, F32, E33, T35, E36, R37, T38, T39, E40, F41, W42, K43, Y45, V46, D47, G48, D49, E52, S53, P55, L57, N58, G59, G60, S61, K63, D64, D65, I66, S68, Y69, E70, W72, P74, F75, G76, F77, E78, G79, K80, E83, L84, D85, V86, T87, I90, K91, N92, G93, R94, E96, F98, K100, S102, A103, D104, K106, V107, V108, S110, T112, E113, G114, Y115, R116, L117, A118, E119, K122, S123, E125, P126, A127, V128, P129, P131, G133, R134, V135, S136, V137, S138, T140, 5141, K142, L143, T144, R145, A146, E147, T148, V149, P151, D152, V153, D154, Y155, V156, S158, T159, E160, A161, E162, T163, I164, L165, D166, I168, T169, S171, T172, S174, F175, D177, F178, T179, R180, V181, V182, G183, G184, E185, D186, A187, K188, P189, G190, F192, P193, W194, V196, V197, L198, N199, G200, K201, V202, D203, A204, F205, G207, G208, S209, I210, V211, E213, K214, W215, I216, V217, T218, A219, A220, V223, E224, T225, G226, V227, K228, I229, T230, V231, V232, A233, G234, E235, I238, E239, E240, T241, E242, T244, E245, K247, R248, V250, I251, R252, I253, I254, P255, Y259, A261, A262, I263, K265, Y266, D269, I270, A271, L272, L273, E274, L275, D276, E277, P278, L279, V280, L281, S283, Y284, V285, T286, P287, I288, I290, A291, D292, K293, E294, Y295, T296, I298, F299, L300, K301, F302, G303, S304, G305, Y306, V307, S308, G309, W310, G311, R312, V313, F314, K316, G317, R318, S319, A320, L321, V322, L323, Y325, L326, R327, V328, P329, L330, V331, D332, R333, A334, T335, L337, R338, S339, T340, K341, F342, T343, I344, Y345, M348, F349, A351, G352, F353, E355, G356, G357, R358, D359, S360, G363, D364, S365, G366, G367, P368, V370, T371, E372, V373, E374, G375, T376, S377, F378, L379, T380, G381, I382, I383, S384, W385, G386, E387, E388, A390, M391, K392, G393, K394, Y395, G396, I397, Y398, T399, K400, V401, S402, R403, Y404, V405, W407, I408, K409, E410, K411, T412, K413, L414, and T415 of a mature FIX polypeptide set forth in SEQ ID NO: 2 or in corresponding loci in an allelic or species variant and/or in a background polypeptide including other modifications.

In one embodiment, positions are typically replaced as follows: replacement of D with N or Q, replacement of E with H, Q or N, replacement of F with I or V, replacement of K with Q or N, replacement of L with I or V, replacement of M with I or V, replacement of N with Q or S, replacement of P with A or S, replacement of R with H or Q, replacement of W with H or S, replacement of Y with I or H, replacement of A, G, I, S, T, or V with Q, H, or N.

In one embodiment, positions corresponding to hFIX are selected (is-HITS) and amino acid replacements are made (LEADs) with increased resistance to proteolysis that include, but are not limited to replacements corresponding to those set forth in Table 5, where the replacements are made compared to the sequence of amino acids set forth in SEQ ID NO: 2. Table 5 provides non-limiting examples of amino acid replacements, corresponding to amino acid positions of a mature FIX polypeptide, that increase resistance to proteolysis and, thereby, protein stability. The modified FIX polypeptides include precursor and mature forms, zymogen and active forms, allelic and species variants and/or modifications in a background FIX polypeptide including other modifications.

In referencing such mutants, the first amino acid (one-letter abbreviation) corresponds to the amino acid that is replaced, the number corresponds to position in the hFIX polypeptide sequence with reference to SEQ ID NO: 2, and the second amino acid (one-letter abbreviation) corresponds to the amino acid selected that replaces the first amino acid at that position. In Table 5 below, the sequence identifier (SEQ ID NO.) is in parenthesis next to each substitution. The FIX polypeptides employed for modification can be any FIX polypeptide, including other mammalian FIX polypeptides. Corresponding positions, as assessed by appropriate alignment, are identified and modified as described herein.

TABLE 5 List of Human FIX Modifications to Increase Resistance to Proteolysis Y1H (3) Y1I (4) K5N (5) K5Q (6) L6I (7) L6V (8) E7Q (9) E7H (10) E7N (11) E8Q (12) E8H (13) E8N (14) F9I (15) F9V (16) L14I (17) L14V (18) E15Q (19) E15H (20) E15N (21) R16H (22) R16Q (23) E17Q (24) E17H (25) E17N (26) M19I (27) M19V (28) E20Q (29) E20H (30) E20N (31) E21Q (32) E21H (33) E21N (34) K22N (35) K22Q (36) F25I (37) F25V (38) E26Q (39) E26H (40) E26N (41) E27Q (42) E27H (43) E27N (44) R29H (45) R29Q (46) E30Q (47) E30H (48) E30N (49) F32I (50) F32V (51) E33Q (52) E33H (53) E33N (54) E36Q (55) E36H (56) E36N (57) R37H (58) R37Q (59) E40Q (60) E40H (61) E40N (62) F41I (63) F41V (64) W42S (65) W42H (66) K43N (67) K43Q (68) Y45H (69) Y45I (70) D47N (71) D47Q (72) D49N (73) D49Q (74) E52Q (75) E52H (76) E52N (77) P55A (78) P55S (79) L57I (80) L57V (81) N58Q (82) N58S (83) K63N (84) K63Q (85) D64N (86) D64Q (87) D65N (88) D65Q (89) Y69H (90) Y69I (91) E70Q (92) E70H (93) E70N (94) W72S (95) W72H (96) P74A (97) P74S (98) F75I (99) F75V (100) F77I (101) F77V (102) E78Q (103) E78H (104) E78N (105) K80N (106) K80Q (107) E83Q (108) E83H (109) E83N (110) L84I (111) L84V (112) D85N (113) D85Q (114) K91N (115) K91Q (116) N92Q (117) N92S (118) R94H (119) R94Q (120) E96Q (121) E96H (122) E96N (123) F98I (124) F98V (125) K100N (126) K100Q (127) D104N (128) D104Q (129) K106N (130) K106Q (131) E113Q (132) E113H (133) E113N (134) Y115H (135) Y115I (136) R116H (137) R116Q (138) L117I (139) L117V (140) E119Q (141) E119H (142) E119N (143) K122N (144) K122Q (145) E125Q (146) E125H (147) E125N (148) P126A (149) P126S (150) P129A (151) P129S (152) P131A (153) P131S (154) R134H (155) R134Q (156) K142N (157) K142Q (158) L143I (159) L143V (160) R145H (161) R145Q (162) E147Q (163) E147H (164) E147N (165) P151A (166) P151S (167) D152N (168) D152Q (169) D154N (170) D154Q (171) Y155H (172) Y155I (173) E160Q (174) E160H (175) E160N (176) E162Q (177) E162H (178) E162N (179) L165I (180) L165V (181) D166N (182) D166Q (183) F175I (184) F175V (185) D177N (186) D177Q (187) F178I (188) F178V (189) R180H (190) R180Q (191) E185Q (192) E185H (193) E185N (194) D186N (195) D186Q (196) K188N (197) K188Q (198) P189A (199) P189S (200) P193A (201) P193S (202) W194S (203) W194H (204) L198I (205) L198V (206) N199Q (207) N199S (208) K201N (209) K201Q (210) D203N (211) D203Q (212) F205I (213) F205V (214) E213Q (215) E213H (216) E213N (217) K214N (218) K214Q (219) W215S (220) W215H (221) E224Q (222) E224H (223) E224N (224) K228N (225) K228Q (226) E235Q (227) E235H (228) E235N (229) E239Q (230) E239H (231) E239N (232) E240Q (233) E240H (234) E240N (235) E242Q (236) E242H (237) E242N (238) E245Q (239) E245H (240) E245N (241) K247N (242) K247Q (243) R248H (244) R248Q (245) R252H (246) R252Q (247) P255A (248) P255S (249) Y259H (250) Y259I (251) K265N (252) K265Q (253) Y266H (254) Y266I (255) D269N (256) D269Q (257) L272I (258) L272V (259) L273I (260) L273V (261) E274Q (262) E274H (263) E274N (264) L275I (265) L275V (266) D276N (267) D276Q (268) E277Q (269) E277H (270) E277N (271) P278A (272) P278S (273) L279I (274) L279V (275) L281I (276) L281V (277) Y284H (278) Y284I (279) P287A (280) P287S (281) D292N (282) D292Q (283) K293N (284) K293Q (285) E294Q (286) E294H (287) E294N (288) Y295H (289) Y295I (290) F299I (291) F299V (292) L300I (293) L300V (294) K301N (295) K301Q (296) F302I (297) F302V (298) Y306H (299) Y306I (300) W310S (301) W310H (302) R312H (303) R312Q (304) F314I (305) F314V (306) K316N (307) K316Q (308) R318H (309) R318Q (310) L321I (311) L321V (312) L323I (313) L323V (314) Y325H (315) Y325I (316) L326I (317) L326V (318) R327H (319) R327Q (320) P329A (321) P329S (322) L330I (323) L330V (324) D332N (325) D332Q (326) R333H (327) R333Q (328) L337I (329) L337V (330) R338H (331) R338Q (332) K341N (333) K341Q (334) F342I (335) F342V (336) Y345H (337) Y345I (338) M348I (339) M348V (340) F349I (341) F349V (342) F353I (343) F353V (344) E355Q (345) E355H (346) E355N (347) R358H (348) R358Q (349) D359N (350) D359Q (351) D364N (352) D364Q (353) P368A (354) P368S (355) E372Q (356) E372H (357) E372N (358) E374Q (359) E374H (360) E374N (361) F378I (362) F378V (363) L379I (364) L379V (365) W385S (366) W385H (367) E387Q (368) E387H (369) E387N (370) E388Q (371) E388H (372) E388N (373) M391I (374) M391V (375) K392N (376) K392Q (377) K394N (378) K394Q (379) Y395H (380) Y395I (381) Y398H (382) Y398I (383) K400N (384) K400Q (385) R403H (386) R403Q (387) Y404H (388) Y404I (389) W407S (390) W407H (391) K409N (392) K409Q (393) E410Q (394) E410H (395) E410N (396) K411N (397) K411Q (398) K413N (399) K413Q (400) L414I (401) L414V (402) S3N (403) S3Q (404) S3H (405) G4N (406) G4Q (407) G4H (408) V10N (409) V10Q (410) V10H (411) G12N (412) G12Q (413) G12H (414) S24N (415) S24Q (416) S24H (417) A28N (418) A28Q (419) A28H (420) V31N (421) V31Q (422) V31H (423) T35N (424) T35Q (425) T35H (426) T38N (427) T38Q (428) T38H (429) T39N (430) T39Q (431) T39H (432) V46N (433) V46Q (434) V46H (435) G48N (436) G48Q (437) G48H (438) S53N (439) S53Q (440) S53H (441) G59N (442) G59Q (443) G59H (444) G60N (445) G60Q (446) G60H (447) S61N (448) S61Q (449) S61H (450) I66N (451) I66Q (452) I66H (453) S68N (454) S68Q (455) S68H (456) G76N (457) G76Q (458) G76H (459) G79N (460) G79Q (461) G79H (462) V86N (463) V86Q (464) V86H (465) T87N (466) T87Q (467) T87H (468) I90N (469) I90Q (470) I90H (471) G93N (472) G93Q (473) G93H (474) S102N (475) S102Q (476) S102H (477) A103N (478) A103Q (479) A103H (480) V107N (481) V107Q (482) V107H (483) V108N (484) V108Q (485) V108H (486) S110N (487) S110Q (488) S110H (489) T112N (490) T112Q (491) T112H (492) G114N (493) G114Q (494) G114H (495) A118N (496) A118Q (497) A118H (498) S123N (499) S123Q (500) S123H (501) A127N (502) A127Q (503) A127H (504) V128N (505) V128Q (506) V128H (507) G133N (508) G133Q (509) G133H (510) V135N (511) V135Q (512) V135H (513) S136N (514) S136Q (515) S136H (516) V137N (517) V137Q (518) V137H (519) S138N (520) S138Q (521) S138H (522) T140N (523) T140Q (524) T140H (525) S141N (526) S141Q (527) S141H (528) T144N (529) T144Q (530) T144H (531) A146N (532) A146Q (533) A146H (534) T148N (535) T148Q (536) T148H (537) V149N (538) V149Q (539) V149H (540) V153N (541) V153Q (542) V153H (543) V156N (544) V156Q (545) V156H (546) S158N (547) S158Q (548) S158H (549) T159N (550) T159Q (551) T159H (552) A161N (553) A161Q (554) A161H (555) T163N (556) T163Q (557) T163H (558) I164N (559) I164Q (560) I164H (561) I168N (562) I168Q (563) I168H (564) T169N (565) T169Q (566) T169H (567) S171N (568) S171Q (569) S171H (570) T172N (571) T172Q (572) T172H (573) S174N (574) S174Q (575) S174H (576) T179N (577) T179Q (578) T179H (579) V181N (580) V181Q (581) V181H (582) V182N (583) V182Q (584) V182H (585) G183N (586) G183Q (587) G183H (588) G184N (589) G184Q (590) G184H (591) A187N (592) A187Q (593) A187H (594) G190N (595) G190Q (596) G190H (597) V196N (598) V196Q (599) V196H (600) V197N (601) V197Q (602) V197H (603) G200N (604) G200Q (605) G200H (606) V202N (607) V202Q (608) V202H (609) A204N (610) A204Q (611) A204H (612) G207N (613) G207Q (614) G207H (615) G208N (616) G208Q (617) G208H (618) S209N (619) S209Q (620) S209H (621) I210N (622) I210Q (623) I210H (624) V211N (625) V211Q (626) V211H (627) I216N (628) I216Q (629) I216H (630) V217N (631) V217Q (632) V217H (633) T218N (634) T218Q (635) T218H (636) A219N (637) A219Q (638) A219H (639) A220N (640) A220Q (641) A220H (642) V223N (643) V223Q (644) V223H (645) T225N (646) T225Q (647) T225H (648) G226N (649) G226Q (650) G226H (651) V227N (652) V227Q (653) V227H (654) I229N (655) I229Q (656) I229H (657) T230N (658) T230Q (659) T230H (660) V231N (661) V231Q (662) V231H (663) V232N (664) V232Q (665) V232H (666) A233N (667) A233Q (668) A233H (669) G234N (670) G234Q (671) G234H (672) I238N (673) I238Q (674) I238H (675) T241N (676) T241Q (677) T241H (678) T244N (679) T244Q (680) T244H (681) V250N (682) V250Q (683) V250H (684) I251N (685) I251Q (686) I251H (687) I253N (688) I253Q (689) I253H (690) I254N (691) I254Q (692) I254H (693) A261N (694) A261Q (695) A261H (696) A262N (697) A262Q (698) A262H (699) I263N (700) I263Q (701) I263H (702) I270N (703) I270Q (704) I270H (705) A271N (706) A271Q (707) A271H (708) V280N (709) V280Q (710) V280H (711) S283N (712) S283Q (713) S283H (714) V285N (715) V285Q (716) V285H (717) T286N (718) T286Q (719) T286H (720) I288N (721) I288Q (722) I288H (723) I290N (724) I290Q (725) I290H (726) A291N (727) A291Q (728) A291H (729) T296N (730) T296Q (731) T296H (732) I298N (733) I298Q (734) I298H (735) G303N (736) G303Q (737) G303H (738) S304N (739) S304Q (740) S304H (741) G305N (742) G305Q (743) G305H (744) V307N (745) V307Q (746) V307H (747) S308N (748) S308Q (749) S308H (750) G309N (751) G309Q (752) G309H (753) G311N (754) G311Q (755) G311H (756) V313N (757) V313Q (758) V313H (759) G317N (760) G317Q (761) G317H (762) S319N (763) S319Q (764) S319H (765) A320N (766) A320Q (767) A320H (768) V322N (769) V322Q (770) V322H (771) V328N (772) V328Q (773) V328H (774) V331N (775) V331Q (776) V331H (777) A334N (778) A334Q (779) A334H (780) T335N (781) T335Q (782) T335H (783) S339N (784) S339Q (785) S339H (786) T340N (787) T340Q (788) T340H (789) T343N (790) T343Q (791) T343H (792) I344N (793) I344Q (794) I344H (795) A351N (796) A351Q (797) A351H (798) G352N (799) G352Q (800) G352H (801) G356N (802) G356Q (803) G356H (804) G357N (805) G357Q (806) G357H (807) S360N (808) S360Q (809) S360H (810) G363N (811) G363Q (812) G363H (813) S365N (814) S365Q (815) S365H (816) G366N (817) G366Q (818) G366H (819) G367N (820) G367Q (821) G367H (822) V370N (823) V370Q (824) V370H (825) T371N (826) T371Q (827) T371H (828) V373N (829) V373Q (830) V373H (831) G375N (832) G375Q (833) G375H (834) T376N (835) T376Q (836) T376H (837) S377N (838) S377Q (839) S377H (840) T380N (841) T380Q (842) T380H (843) G381N (844) G381Q (845) G381H (846) I382N (847) I382Q (848) I382H (849) I383N (850) I383Q (851) I383H (852) S384N (853) S384Q (854) S384H (855) G386N (856) G386Q (857) G386H (858) A390N (859) A390Q (860) A390H (861) G393N (862) G393Q (863) G393H (864) G396N (865) G396Q (866) G396H (867) I397N (868) I397Q (869) I397H (870) T399N (871) T399Q (872) T399H (873) V401N (874) V401Q (875) V401H (876) S402N (877) S402Q (878) S402H (879) V405N (880) V405Q (881) V405H (882) I408N (883) I408Q (884) I408H (885) T412N (886) T412Q (887) T412H (888) T415N (889) T415Q (890) T415H (891) L165Q (1025) L165H (1026) F175H (1027) F178H (1028) F192H (1029) F192I (1030) F192V (1031) W194I (1032) L198Q (1033) L198H (1034)

A modified FIX polypeptide provided herein that exhibits increased protease resistance can contain one or more amino acid modifications corresponding to any one or more modifications of Y1H (i.e., replacement of Y by H at a position corresponding to amino acid position 1 of mature human FIX (such as, SEQ ID NO: 2)), Y1I, S3Q, S3H, S3N, G4Q, G4H, G4N, K5N, K5Q, L6I, L6V, E7Q, E7H, E7N, E8Q, E8H, E8N, F91, F9V, V10Q, V10H, V10N, G12Q, G12H, G12N, L14I, L14V, E15Q, E15H, E15N, R16H, R16Q, E17Q, E17H, E17N, M191, M19V, E20Q, E20H, E20N, E21Q, E21H, E21N, K22N, K22Q, S24Q, S24H, S24N, F25I, F25V, E26Q, E26H, E26N, E27Q, E27H, E27N, A28Q, A28H, A28N, R29H, R29Q, E30Q, E30H, E30N, V31Q, V31H, V31N, F32I, F32V, E33Q, E33H, E33N, T35Q, T35H, T35N, E36Q, E36H, E36N, R37H, R37Q, T38Q, T38H, T38N, T39Q, T39H, T39N, E40Q, E40H, E40N, F41I, F41V, W42S, W42H, K43N, K43Q, Y45H, Y45I, V46Q, V46H, V46N, D47N, D47Q, G48Q, G48H, G48N, D49N, D49Q, E52Q, E52H, E52N, S53Q, S53H, S53N, P55A, P55S, L57I, L57V, N58Q, N58S, G59Q, G59H, G59N, G60Q, G60H, G60N, S61Q, S61H, S61N, K63N, K63Q, D64N, D64Q, D65N, D65Q, 166Q, 166H, 166N, S68Q, S68H, S68N, Y69H, Y69I, E70Q, E70H, E70N, W72S, W72H, P74A, P74S, F75I, F75V, G76Q, G76H, G76N, F771, F77V, E78Q, E78H, E78N, G79Q, G79H, G79N, K80N, K80Q, E83Q, E83H, E83N, L84I, L84V, D85N, D85Q, V86Q, V86H, V86N, T87Q, T87H, T87N, 190Q, 190H, 190N, K91N, K91Q, N92Q, N92S, G93Q, G93H, G93N, R94H, R94Q, E96Q, E96H, E96N, F981, F98V, K100N, K100Q, S102Q, S102H, S102N, A103Q, A103H, A103N, D104N, D104Q, K106N, K106Q, V107Q, V107H, V107N, V108Q, V108H, V108N, S110Q, S110H, S110N, T112Q, T112H, T112N, E113Q, E113H, E113N, G114Q, G114H, G114N, Y115H, Y115I, R116H, R116Q, L117I, L117V, A118Q, A118H, A118N, E119Q, E119H, E119N, K122N, K122Q, S123Q, S123H, S123N, E125Q, E125H, E125N, P126A, P126S, A127Q, A127H, A127N, V128Q, V128H, V128N, P129A, P129S, P131A, P131S, G133Q, G133H, G133N, R134H, R134Q, V135Q, V135H, V135N, S136Q, S136H, S136N, V137Q, V137H, V137N, S138Q, S138H, S138N, T140Q, T140H, T140N, S141Q, S141H, S141N, K142N, K142Q, L143I, L143V, T144Q, T144H, T144N, R145H, R145Q, A146Q, A146H, A146N, E147Q, E147H, E147N, T148Q, T148H, T148N, V149Q, V149H, V149N, P151A, P151S, D152N, D152Q, V153Q, V153H, V153N, D154N, D154Q, Y155H, Y155I, V156Q, V156H, V156N, S158Q, S158H, S158N, T159Q, T159H, T159N, E160Q, E160H, E160N, A161Q, A161H, A161N, E162Q, E162H, E162N, T163Q, T163H, T163N, I164Q, I164H, I164N, L165I, L165V, L165Q, L165H, D166N, D166Q, I168Q, I168H, I168N, T169Q, T169H, T169N, S171Q, S171H, S171N, T172Q, T172H, T172N, S174Q, S174H, S174N, F175I, F175V, F175H, D177N, D177Q, F178I, F178V, F178H, T179Q, T179H, T179N, R180H, R180Q, V181Q, V181H, V181N, V182Q, V182H, V182N, G183Q, G183H, G183N, G184Q, G184H, G184N, E185Q, E185H, E185N, D186N, D186Q, A187Q, A187H, A187N, K188N, K188Q, P189A, P189S, G190Q, G190H, G190N, F192I, F192V, F192IH, P193A, P193S, W194S, W194H, W194I, V196Q, V196H, V196N, V197Q, V197H, V197N, L198I, L198V, L198Q, L198H, N199Q, N199S, G200Q, G200H, G200N, K201N, K201Q, V202Q, V202H, V202N, D203N, D203Q, A204Q, A204H, A204N, F205I, F205V, G207Q, G207H, G207N, G208Q, G208H, G208N, S209Q, S209H, S209N, I210Q, I210H, I210N, V211Q, V211H, V211N, E213Q, E213H, E213N, K214N, K214Q, W215S, W215H, I216Q, I216H, I216N, V217Q, V217H, V217N, T218Q, T218H, T218N, A219Q, A219H, A219N, A220Q, A220H, A220N, V223Q, V223H, V223N, E224Q, E224H, E224N, T225Q, T225H, T225N, G226Q, G226H, G226N, V227Q, V227H, V227N, K228N, K228Q, I229Q, I229H, I229N, T230Q, T230H, T230N, V231Q, V231H, V231N, V232Q, V232H, V232N, A233Q, A233H, A233N, G234Q, G234H, G234N, E235Q, E235H, E235N, I238Q, I238H, I238N, E239Q, E239H, E239N, E240Q, E240H, E240N, T241Q, T241H, T241N, E242Q, E242H, E242N, T244Q, T244H, T244N, E245Q, E245H, E245N, K247N, K247Q, R248H, R248Q, V250Q, V250H, V250N, I251Q, I251H, I251N, R252H, R252Q, I253Q, I253H, I253N, I254Q, I254H, I254N, P255A, P255S, Y259H, Y259I, A261Q, A261H, A261N, A262Q, A262H, A262N, I263Q, I263H, I263N, K265N, K265Q, Y266H, Y266I, D269N, D269Q, I270Q, I270H, I270N, A271Q, A271H, A271N, L272I, L272V, L273I, L273V, E274Q, E274H, E274N, L275I, L275V, D276N, D276Q, E277Q, E277H, E277N, P278A, P278S, L279I, L279V, V280Q, V280H, V280N, L281I, L281V, S283Q, S283H, S283N, Y284H, Y284I, V285Q, V285H, V285N, T286Q, T286H, T286N, P287A, P287S, I288Q, I288H, I288N, I290Q, I290H, I290N, A291Q, A291H, A291N, D292N, D292Q, K293N, K293Q, E294Q, E294H, E294N, Y295H, Y295I, T296Q, T296H, T296N, I298Q, I298H, I298N, F299I, F299V, L300I, L300V, K301N, K301Q, F302I, F302V, G303Q, G303H, G303N, S304Q, S304H, S304N, G305Q, G305H, G305N, Y306H, Y306I, V307Q, V307H, V307N, S308Q, S308H, S308N, G309Q, G309H, G309N, W310S, W310H, G311Q, G311H, G311N, R312H, R312Q, V313Q, V313H, V313N, F314I, F314V, K316N, K316Q, G317Q, G317H, G317N, R318H, R318Q, S319Q, S319H, S319N, A320Q, A320H, A320N, L321I, L321V, V322Q, V322H, V322N, L323I, L323V, Y325H, Y325I, L326I, L326V, R327H, R327Q, V328Q, V328H, V328N, P329A, P329S, L330I, L330V, V331Q, V331H, V331N, D332N, D332Q, R333H, R333Q, A334Q, A334H, A334N, T335Q, T335H, T335N, L337I, L337V, R338H, R338Q, S339Q, S339H, S339N, T340Q, T340H, T340N, K341N, K341Q, F342I, F342V, T343Q, T343H, T343N, I344Q, I344H, I344N, Y345H, Y345I, M348I, M348V, F349I, F349V, A351Q, A351H, A351N, G352Q, G352H, G352N, F353I, F353V, E355Q, E355H, E355N, G356Q, G356H, G356N, G357Q, G357H, G357N, R358H, R358Q, D359N, D359Q, S360Q, S360H, S360N, G363Q, G363H, G363N, D364N, D364Q, S365Q, S365H, S365N, G366Q, G366H, G366N, G367Q, G367H, G367N, P368A, P368S, V370Q, V370H, V370N, T371Q, T371H, T371N, E372Q, E372H, E372N, V373Q, V373H, V373N, E374Q, E374H, E374N, G375Q, G375H, G375N, T376Q, T376H, T376N, S377Q, S377H, S377N, F378I, F378V, L379I, L379V, T380Q, T380H, T380N, G381Q, G381H, G381N, I382Q, I382H, I382N, I383Q, I383H, I383N, S384Q, S384H, S384N, W385S, W385H, G386Q, G386H, G386N, E387Q, E387H, E387N, E388Q, E388H, E388N, A390Q, A390H, A390N, M391I, M391V, K392N, K392Q, G393Q, G393H, G393N, K394N, K394Q, Y395H, Y395I, G396Q, G396H, G396N, I397Q, I397H, I397N, Y398H, Y398I, T399Q, T399H, T399N, K400N, K400Q, V401Q, V401H, V401N, S402Q, S402H, S402N, R403H, R403Q, Y404H, Y404I, V405Q, V405H, V405N, W407S, W407H, I408Q, I408H, I408N, K409N, K409Q, E410Q, E410H, E410N, K411N, K411Q, T412Q, T412H, T412N, K413N, K413Q, L414I, L414V, T415Q, T415H, and T415N, where the modified polypeptide exhibits increased resistance to proteolysis. In some examples, the modifications are in an unmodified FIX polypeptide, such as a FIX having a sequence of amino acids set forth in SEQ ID NO: 2. Exemplary modified FIX LEAD candidate polypeptides are set forth in any one of SEQ ID NOS: 3-891 or 1025-1034. In some examples, the modifications are in a FIX polypeptide, such as a FIX polypeptide having a sequence of amino acids set forth in SEQ ID NO: 892 or 1035. For example, exemplary modified FIX LEAD candidate polypeptides are set forth in any one of SEQ ID NOS: 1036-1926 or 2035-2044.

Additionally, a modified FIX polypeptide as set forth above can contain a further modification compared to an unmodified FIX polypeptide. Generally, the resulting modified FIX polypeptide retains one or more activities of the unmodified FIX polypeptide. In some embodiments, the modified FIX polypeptide inhibits the activity of an unmodified or wild-type FIX polypeptide and/or acts as an anticoagulant.

i. Modified FIX Polypeptides Exhibiting Increased Protease Resistance to Elastase

Exemplary of modified FIX polypeptides exhibiting increased protease resistance are FIX polypeptides exhibiting increased resistance to elastase. Non-limiting modifications in a FIX polypeptide that confer increased resistance to elastase have been rationally determined herein based on the known substrate specificity of elastase. Polypeptides are cleaved by elastase at or near a sequence of small hydrophobic chains. Modifications that render polypeptides more resistant to hydrolysis by elastase are provided. Of the modifications disclosed in Table 5, some are more specific to resistance to protease digestion by elastase. The following is-HIT positions were identified to eliminate elastase sensitive sites and increase protein stability of FIX polypeptides: 3, 4, 10, 12, 24, 28, 31, 35, 38, 39, 46, 48, 53, 59, 60, 61, 66, 68, 76, 79, 86, 87, 90, 93, 102, 103, 107, 108, 110, 112, 114, 118, 123, 127, 128, 133, 135, 136, 137, 138, 140, 141, 144, 146; 148, 149, 153, 156, 158, 159, 161, 163, 164, 168, 169, 171, 172, 174, 179, 181, 182, 183, 184, 187, 190, 196, 197, 200, 202, 204, 207, 208, 209, 210, 211, 216, 217, 218, 219, 220, 223, 225, 226, 227, 229, 230, 231, 232, 233, 234, 238, 241, 244, 250, 251, 253, 254, 261, 262, 263, 270, 271, 280, 283, 285, 286, 288, 290, 291, 296, 298, 303, 304, 305, 307, 308, 309, 311, 313, 317, 319, 320, 322, 328, 331, 334, 335, 339, 340, 343, 344, 351, 352, 356, 357, 360, 363, 365, 366, 367, 370, 371, 373, 375, 376, 377, 380, 381, 382, 383, 384, 386, 390, 393, 396, 397, 399, 401, 402, 405, 408, 412, and 415, corresponding to amino acid positions in a mature FIX polypeptide set forth in SEQ ID NO: 2. Amino acid modifications can be at any one or more positions corresponding to any of the following positions: S3, G4, V10, G12, S24, A28, V31, T35, T38, T39, V46, G48, S53, G59, G60, S61, I66, S68, G76, G79, V86, T87, I90, G93, S102, A103, V107, V108, S110, T112, G114, A118, S123, A127, V128, G133, V135, S136, V137, S138, T140, S141, T144, A146, T148, V149, V153, V156, S158, T159, A161, T163, I164, 1168, T169, S171, T172, S174, T179, V181, V182, G183, G184, A187, G190, V196, V197, G200, V202, A204, G207, G208, S209, I210, V211, I216, V217, T218, A219, A220, V223, T225, G226, V227, I229, T230, V231, V232, A233, G234, I238, T241, T244, V250, I251, I253, I254, A261, A262, I263, I270, A271, V280, S283, V285, T286, I288, I290, A291, T296, I298, G303, S304, G305, V307, S308, G309, G311, V313, G317, S319, A320, V322, V328, V331, A334, T335, S339, T340, T343, I344, A351, G352, G356, G357, S360, G363, S365, G366, G367, V370, T371, V373, G375, T376, S377, T380, G381, I382, I383, S384, G386, A390, G393, I396, I397, T399, V401, S402, V405, I408, T412, and T415, of a mature FIX polypeptide set forth in SEQ ID NO: 2. Other candidate Leads can be obtained by replacement or replacements of amino acids at is-HIT positions such as, but not limited to, amino acid modifications as described for candidate LEADs in Table 6. Candidate leads can be empirically tested to determine those that confer resistance to elastase. Table 6 provides non-limiting examples of amino acid modifications that are more specific to resistance to protease digestion by elastase and, thereby, increase protein stability. Generally, a resulting modified FIX polypeptide retains one or more activities of a mature or unmodified FIX polypeptide. In some embodiments, the modified FIX polypeptide inhibits an activity of an unmodified or wild-type FIX polypeptide and/or acts as an anticoagulant. In Table 6 below, the sequence identifier (SEQ ID NO.) is in parenthesis next to each substitution.

TABLE 6 List of Human FIX Modifications to Increase Resistance to Elastase Proteolysis S3N (403) S3Q (404) S3H (405) G4N (406) G4Q (407) G4H (408) V10N (409) V10Q (410) V10H (411) G12N (412) G12Q (413) G12H (414) S24N (415) S24Q (416) S24H (417) A28N (418) A28Q (419) A28H (420) V31N (421) V31Q (422) V31H (423) T35N (424) T35Q (425) T35H (426) T38N (427) T38Q (428) T38H (429) T39N (430) T39Q (431) T39H (432) V46N (433) V46Q (434) V46H (435) G48N (436) G48Q (437) G48H (438) S53N (439) S53Q (440) S53H (441) G59N (442) G59Q (443) G59H (444) G60N (445) G60Q (446) G60H (447) S61N (448) S61Q (449) S61H (450) I66N (451) I66Q (452) I66H (453) S68N (454) S68Q (455) S68H (456) G76N (457) G76Q (458) G76H (459) G79N (460) G79Q (461) G79H (462) V86N (463) V86Q (464) V86H (465) T87N (466) T87Q (467) T87H (468) I90N (469) I90Q (470) I90H (471) G93N (472) G93Q (473) G93H (474) S102N (475) S102Q (476) S102H (477) A103N (478) A103Q (479) A103H (480) V107N (481) V107Q (482) V107H (483) V108N (484) V108Q (485) V108H (486) S110N (487) S110Q (488) S110H (489) T112N (490) T112Q (491) T112H (492) G114N (493) G114Q (494) G114H (495) A118N (496) A118Q (497) A118H (498) S123N (499) S123Q (500) S123H (501) A127N (502) A127Q (503) A127H (504) V128N (505) V128Q (506) V128H (507) G133N (508) G133Q (509) G133H (510) V135N (511) V135Q (512) V135H (513) S136N (514) S136Q (515) S136H (516) V137N (517) V137Q (518) V137H (519) S138N (520) S138Q (521) S138H (522) T140N (523) T140Q (524) T140H (525) S141N (526) S141Q (527) S141H (528) T144N (529) T144Q (530) T144H (531) A146N (532) A146Q (533) A146H (534) T148N (535) T148Q (536) T148H (537) V149N (538) V149Q (539) V149H (540) V153N (541) V153Q (542) V153H (543) V156N (544) V156Q (545) V156H (546) S158N (547) S158Q (548) S158H (549) T159N (550) T159Q (551) T159H (552) A161N (553) A161Q (554) A161H (555) T163N (556) T163Q (557) T163H (558) I164N (559) I164Q (560) I164H (561) I168N (562) I168Q (563) I168H (564) T169N (565) T169Q (566) T169H (567) S171N (568) S171Q (569) S171H (570) T172N (571) T172Q (572) T172H (573) S174N (574) S174Q (575) S174H (576) T179N (577) T179Q (578) T179H (579) V181N (580) V181Q (581) V181H (582) V182N (583) V182Q (584) V182H (585) G183N (586) G183Q (587) G183H (588) G184N (589) G184Q (590) G184H (591) A187N (592) A187Q (593) A187H (594) G190N (595) G190Q (596) G190H (597) V196N (598) V196Q (599) V196H (600) V197N (601) V197Q (602) V197H (603) G200N (604) G200Q (605) G200H (606) V202N (607) V202Q (608) V202H (609) A204N (610) A204Q (611) A204H (612) G207N (613) G207Q (614) G207H (615) G208N (616) G208Q (617) G208H (618) S209N (619) S209Q (620) S209H (621) I210N (622) I210Q (623) I210H (624) V211N (625) V211Q (626) V211H (627) I216N (628) I216Q (629) I216H (630) V217N (631) V217Q (632) V217H (633) T218N (634) T218Q (635) T218H (636) A219N (637) A219Q (638) A219H (639) A220N (640) A220Q (641) A220H (642) V223N (643) V223Q (644) V223H (645) T225N (646) T225Q (647) T225H (648) G226N (649) G226Q (650) G226H (651) V227N (652) V227Q (653) V227H (654) I229N (655) I229Q (656) I229H (657) T230N (658) T230Q (659) T230H (660) V231N (661) V231Q (662) V231H (663) V232N (664) V232Q (665) V232H (666) A233N (667) A233Q (668) A233H (669) G234N (670) G234Q (671) G234H (672) I238N (673) I238Q (674) I238H (675) T241N (676) T241Q (677) T241H (678) T244N (679) T244Q (680) T244H (681) V250N (682) V250Q (683) V250H (684) I251N (685) I251Q (686) I251H (687) I253N (688) I253Q (689) I253H (690) I254N (691) I254Q (692) I254H (693) A261N (694) A261Q (695) A261H (696) A262N (697) A262Q (698) A262H (699) I263N (700) I263Q (701) I263H (702) I270N (703) I270Q (704) I270H (705) A271N (706) A271Q (707) A271H (708) V280N (709) V280Q (710) V280H (711) S283N (712) S283Q (713) S283H (714) V285N (715) V285Q (716) V285H (717) T286N (718) T286Q (719) T286H (720) I288N (721) I288Q (722) I288H (723) I290N (724) I290Q (725) I290H (726) A291N (727) A291Q (728) A291H (729) T296N (730) T296Q (731) T296H (732) I298N (733) I298Q (734) I298H (735) G303N (736) G303Q (737) G303H (738) S304N (739) S304Q (740) S304H (741) G305N (742) G305Q (743) G305H (744) V307N (745) V307Q (746) V307H (747) S308N (748) S308Q (749) S308H (750) G309N (751) G309Q (752) G309H (753) G311N (754) G311Q (755) G311H (756) V313N (757) V313Q (758) V313H (759) G317N (760) G317Q (761) G317H (762) S319N (763) S319Q (764) S319H (765) A320N (766) A320Q (767) A320H (768) V322N (769) V322Q (770) V322H (771) V328N (772) V328Q (773) V328H (774) V331N (775) V331Q (776) V331H (777) A334N (778) A334Q (779) A334H (780) T335N (781) T335Q (782) T335H (783) S339N (784) S339Q (785) S339H (786) T340N (787) T340Q (788) T340H (789) T343N (790) T343Q (791) T343H (792) I344N (793) I344Q (794) I344H (795) A351N (796) A351Q (797) A351H (798) G352N (799) G352Q (800) G352H (801) G356N (802) G356Q (803) G356H (804) G357N (805) G357Q (806) G357H (807) S360N (808) S360Q (809) S360H (810) G363N (811) G363Q (812) G363H (813) S365N (814) S365Q (815) S365H (816) G366N (817) G366Q (818) G366H (819) G367N (820) G367Q (821) G367H (822) V370N (823) V370Q (824) V370H (825) T371N (826) T371Q (827) T371H (828) V373N (829) V373Q (830) V373H (831) G375N (832) G375Q (833) G375H (834) T376N (835) T376Q (836) T376H (837) S377N (838) S377Q (839) S377H (840) T380N (841) T380Q (842) T380H (843) G381N (844) G381Q (845) G381H (846) I382N (847) I382Q (848) I382H (849) I383N (850) I383Q (851) I383H (852) S384N (853) S384Q (854) S384H (855) G386N (856) G386Q (857) G386H (858) A390N (859) A390Q (860) A390H (861) G393N (862) G393Q (863) G393H (864) G396N (865) G396Q (866) G396H (867) I397N (868) I397Q (869) I397H (870) T399N (871) T399Q (872) T399H (873) V401N (874) V401Q (875) V401H (876) S402N (877) S402Q (878) S402H (879) V405N (880) V405Q (881) V405H (882) I408N (883) I408Q (884) I408H (885) T412N (886) T412Q (887) T412H (888) T415N (889) T415Q (890) T415H (891)

A modified FIX polypeptide provided herein that exhibits increased protease resistance to elastase can contain one or more amino acid modifications corresponding to modifications selected from any of S3Q, S3H, S3N, G4Q, G4H, 04N, V10Q, V10H, V10N, G12Q, G12H, G12N, S24Q, S24H, S24N, A28Q, A28H, A28N, V31Q, V31H, V31N, T35Q, T35H, T35N, T38Q, T38H, T38N, T39Q, T39H, T39N, V46Q, V46H, V46N, G48Q, G48H, G48N, S53Q, S53H, S53N, G59Q, G59H, G59N, G60Q, G60H, G60N, S61Q, S61H, S61N, 166Q, 166H, 166N, S68Q, S68H, S68N, G76Q, G76H, G76N, G79Q, G79H, G79N, V86Q, V86H, V86N, T87Q, T87H, T87N, 190Q, 190H, 190N, G93Q, G93H, G93N, S102Q, S102H, S102N, A103Q, A103H, A103N, V107Q, V107H, V107N, V108Q, V108H, V108N, S110Q, S110H, S110N, T112Q, T112H, T112N, G114Q, G114H, G114N, A118Q, A118H, A118N, S123Q, S123H, S123N, A127Q, A127H, A127N, V128Q, V128H, V128N, G133Q, G133H, G133N, V135Q, V135H, V135N, S136Q, S136H, S136N, V137Q, V137H, V137N, S138Q, S138H, S138N, T140Q, T140H, T140N, S141Q, S141H, S141N, T144Q, T144H, T144N, A146Q, A146H, A146N, T148Q, T14811, T148N, V149Q, V149H, V149N, V153Q, V153H, V153N, V156Q, V156H, V156N, S158Q, S158H, S158N, T159Q, T159H, T159N, A161Q, A161H, A161N, T163Q, T163H, T163N, I164Q, I164H, I164N, I168Q, I168H, I168N, T169Q, T169H, T169N, S171Q, S171H, S171N, T172Q, T172H, T172N, S174Q, S174H, S174N, T179Q, T179H, T179N, V181Q, V181H, V181N, V182Q, V182H, V182N, G183Q, G183H, G183N, G184Q, G184H, G184N, A187Q, A187H, A187N, G190Q, G190H, G190N, V196Q, V196H, V196N, V197Q, V197H, V19′7N, G200Q, G200H, G200N, V202Q, V202H, V202N, A204Q, A204H, A204N, G207Q, G207H, G207N, G208Q, G208H, G208N, S209Q, S209H, S209N, I210Q, I210H, I210N, V211Q, V21111, V211N, I216Q, I216H, I216N, V217Q, V217H, V217N, T218Q, T218H, T218N, A219Q, A219H, A219N, A220Q, A220H, A220N, V223Q, V223H, V223N, T225Q, T225H, T225N, G226Q, G226H, G226N, V227Q, V227H, V227N, I229Q, I229H, I229N, T230Q, T230H, T230N, V231Q, V231H, V231N, V232Q, V232H, V232N, A233Q, A233H, A233N, G234Q, G234H, G234N, I238Q, I238H, I238N, T241Q, T241H, T241N, T244Q, T244H, T244N, V250Q, V250H, V250N, I251Q, I251H, I251N, I253Q, I253H, I253N, I254Q, I254H, I254N, A261Q, A261H, A261N, A262Q, A262H, A262N, I263Q, I263H, I263N, I270Q, I270H, I270N, A271Q, A271H, A271N, V280Q, V280H, V280N, S283Q, S283H, S283N, V285Q, V285H, V285N, T286Q, T286H, T286N, I288Q, I288H, I288N, I290Q, I290H, I290N, A291Q, A291H, A291N, T296Q, T296H, T296N, I298Q, I298H, I298N, G303Q, G303H, G303N, S304Q, S304H, S304N, G305Q, G305H, G305N, V307Q, V307H, V307N, S308Q, S308H, S308N, G309Q, G309H, G309N, G311Q, G311H, G311N, V313Q, V313H, V313N, G317Q, G317H, G317N, S319Q, S319H, S319N, A320Q, A320H, A320N, V322Q, V322H, V322N, V328Q, V328H, V328N, V331Q, V331H, V331N, A334Q, A334H, A334N, T335Q, T335H, T335N, S339Q, S339H, S339N, T340Q, T340H, T340N, T343Q, T343H, T343N, I344Q, I344H, I344N, A351Q, A351H, A351N, G352Q, G352H, G352N, G356Q, G356H, G356N, G357Q, G357H, G357N, S360Q, S360H, S360N, G363Q, G363H, G363N, S365Q, S365H, S365N, G366Q, G366H, G366N, G367Q, G367H, G367N, V370Q, V370H, V370N, T371Q, T371H, T371N, V373Q, V373H, V373N, G375Q, G375H, G375N, T376Q, T376H, T376N, S377Q, S377H, S377N, T380Q, T380H, T380N, G381Q, G381H, G381N, I382Q, I382H, I382N, I383Q, I383H, I383N, S384Q, S384H, S384N, G386Q, G386H, G386N, A390Q, A390H, A390N, G393Q, G393H, G393N, G396Q, G396H, G396N, I397Q, I397H, I397N, T399Q, T399H, T399N, V401Q, V401H, V401N, S402Q, S402H, S402N, V405Q, V405H, V405N, I408Q, I408H, I408N, T412Q, T412H, T412N, T415Q, T415H, T415N of a mature FIX polypeptide set forth in SEQ ID NO: 2. In some examples, the modifications are in a FIX polypeptide having a sequence of amino acids set forth in SEQ ID NO: 2. Exemplary modified FIX candidate LEAD polypeptides are set forth in any one of SEQ ID NOS: 3-891 or 1025-1034. In some examples, the modifications are in a FIX polypeptide, such as a FIX polypeptide having a sequence of amino acids set forth in SEQ ID NO: 892 or 1035. For example, exemplary modified FIX LEAD candidate polypeptides are set forth in any one of SEQ ID NOS: 1036-1926 or 2035-2044.

e. Assessment of FIX Variants with Increased Resistance to Proteolysis

Increased resistance to proteolysis of FIX variants can be assessed by any methods known in the art to assess protein stability, thermal tolerance, protease sensitivity and resistance and/or FIX activity. In one example, protease resistance is measured by incubating a modified FIX polypeptide with one or more proteases and then assessing residual activity compared to an untreated control. A modified FIX can be compared with an unmodified and/or wild-type native FIX treated under similar conditions to determine if the particular variant retains more activity than the unmodified FIX. Activity can be assessed by any methods known in the art, for example by measuring coagulation activities.

Kinetic studies of protease resistance also can be used to assess a modified FIX polypeptide. For example, a modified FIX polypeptide is incubated with one or more proteases and samples are taken over a series of time-points. At each time point, the proteases are inactivated and the samples are then tested for FIX activity. In one embodiment, the modified polypeptide is at least about or 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200%, 300%, 400%, 500%, or more resistant to proteolysis.

In one exemplary embodiment, FIX variants are assessed for protease resistance with a mixture of proteases and proteolytic conditions including pepsin, trypsin, chymotrypsin, elastase, aminopeptidase, gelatinase B, gelatinase A, α-chymotrypsin, carboxypeptidase, endoproteinase Arg-C, endoproteinase Asp-N, endoproteinase Glu-C, endoproteinase Lys-C, luminal pepsin, microvillar endopeptidase, dipeptidyl peptidase, enteropeptidase, hydrolase, NS3, factor Xa, Granzyme B, thrombin, plasmin, urokinase, tPA and PSA. For example, a cytopathic effects (CPE) assay can be used to assess coagulation activity of modified FIX polypeptides compared to unmodified FIX polypeptides. Specifically, coagulation activity of FIX can determined by the capacity of the modified FIX polypeptides to induce formation of a clot in an assay, such as an activated partial thromboplastin time assay. The resistance of the modified FIX polypeptides compared to wild-type FIX against enzymatic cleavage can be analyzed by mixing FIX polypeptides with proteases. After exposure to proteases, coagulation activities can be assessed.

In one example, activity of modified hFIX is assessed in an assay by measuring the capacity of the modified hFIX to modulate coagulation when added to the sample. Prior to the measurement of activity, hFIX molecules can be challenged with proteases (blood, intestinal, etc.) including conditions mimicking administered conditions, such as serum, blood, saliva, or digestive assays (in vitro assays), and/or administered to a subject such as a mouse or human (in vivo assays) during different incubation or post-injection times. The activity measured, corresponds then to the residual activity following exposure to the proteolytic mixtures. Activity can be compared with an unmodified FIX as a measurement of the effect of the modification on protease stability and on the activity. In one example, the unmodified FIX is a wild-type native FIX. In another example, the unmodified FIX is a variant form of FIX that was used as a starting material to introduce further modifications. Modified FIX polypeptides also can be compared with any known FIX polypeptide in any assay known in the art to compare protease sensitivity, thermal tolerance and/or any other activity.

2. Super-LEADs

Modification of FIX polypeptides also can include combining two or more modifications as set forth above. Modified FIX super-LEAD polypeptides are a combination of single amino acid mutations present in two or more of the respective modified FIX LEAD polypeptides. Thus, modified FIX super-LEAD polypeptides have two or more of the single amino acid replacements derived from two or more of the respective modified FIX LEAD polypeptides. As described above and in detail below, modified FIX polypeptides provided herein exhibit increased protein stability manifested as an increased resistance to proteolysis. Typically, modified FIX LEAD polypeptides created are those whose performance has been optimized with respect to the unmodified polypeptide by modification of a single amino acid replacement at one is-HIT position. Modified FIX super-Lead polypeptides are created such that the polypeptide contains two or more FIX LEAD modifications, each at a different is-HIT position. Modifications that increase proteolysis resistance can be added to other modifications provided herein or known in the art to increase proteolysis resistance. In one example, modifications that increase stability can be added to other modifications provided herein or known in the art to increase protein stability. In another example, modifications that increase stability can be added to modifications provided herein or known in the art to increase proteolysis resistance. Modifications that increase protease resistance and/or stability also can be added to modifications to FIX that alter other functionalities including activity, modifications that affect post-translation protein modifications and any other known modifications in the art.

Once the modified LEAD polypeptides have been identified using, for example, 2D-scanning methods, super-LEADs can be generated by combining two or more individual LEADs using methods well known in the art, such as recombination, mutagenesis and DNA shuffling, and by methods such as additive directional mutagenesis, 3D-scanning, and multi-overlapped primer extensions, as provided above.

Exemplary modified FIX super-LEAD polypeptides exhibiting increased protein stability can include FIX polypeptides containing two or more amino acid modifications as compared to an unmodified FIX polypeptide. In some examples, a FIX polypeptide can contain 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more modified positions. Generally, the resulting FIX polypeptide exhibits increased protein stability and retains at least one activity of an unmodified FIX polypeptide. A modified FIX polypeptide can include any two or more amino acid modifications set forth in Table 5 above. For example, the modified FIX polypeptide can contain two or more amino acid modifications corresponding to any two or more modifications of Y1I, S3Q, S3H, S3N, G4Q, G4H, G4N, K5N, K5Q, L6I, L6V, E7Q, E7H, E7N, E8Q, E8H, E8N, F9I, F9V, V10Q, V10H, V10N, G12Q, G12H, G12N, L14I, L14V, E15Q, E15H, E15N, R16H, R16Q, E17Q, E17H, E17N, M19I, M19V, E20Q, E20H, E20N, E21Q, E21H, E21N, K22N, K22Q, S24Q, S24H, S24N, F25I, F25V, E26Q, E26H, E26N, E27Q, E27H, E27N, A28Q, A28H, A28N, R29H, R29Q, E30Q, E30H, E30N, V31Q, V31H, V31N, F321, F32V, E33Q, E33H, E33N, T35Q, T35H, T35N, E36Q, E36H, E36N, R37H, R37Q, T38Q, T38H, T38N, T39Q, T39H, T39N, E40Q, E40H, E40N, F41I, F41V, W42S, W42H, K43N, K43Q, Y45H, Y451, V46Q, V46H, V46N, D47N, D47Q, G48Q, G48H, G48N, D49N, D49Q, E52Q, E52H, E52N, S53Q, S53H, S53N, P55A, P55S, L571, L57V, N58Q, N58S, G59Q, G59H, G59N, G60Q, G60H, G60N, S61Q, S61H, S61N, K63N, K63Q, D64N, D64Q, D65N, D65Q, 166Q, 166H, 166N, S68Q, S68H, S68N, Y69H, Y69I, E70Q, E70H, E70N, W72S, W72H, P74A, P74S, F751, F75V, G76Q, G76H, G76N, F77I, F77V, E78Q, E78H, E78N, G79Q, G79H, G79N, K80N, K80Q, E83Q, E83H, E83N, L84I, L84V, D85N, D85Q, V86Q, V86H, V86N, T87Q, T87H, T87N, 190Q, 190H, 190N, K91N, K91Q, N92Q, N92S, G93Q, G93H, G93N, R94H, R94Q, E96Q, E96H, E96N, F98I, F98V, K100N, K100Q, S102Q, S102H, S102N, A103Q, A103H, A103N, D104N, D104Q, K106N, K106Q, V107Q, V107H, V10′7N, V108Q, V108H, V108N, S110Q, S110H, S110N, T112Q, T112H, T112N, E113Q, E113H, E113N, G114Q, G114H, G114N, Y115H, Y115I, R116H, R116Q, L117I, L117V, A118Q, A118H, A118N, E119Q, E119H, E119N, K122N, K122Q, S123Q, S123H, S123N, E125Q, E125H, E125N, P126A, P126S, A127Q, A127H, A127N, V128Q, V128H, V128N, P129A, P129S, P131A, P131S, G133Q, G133H, G133N, R134H, R134Q, V135Q, V135H, V135N, S136Q, S136H, S136N, V137Q, V137H, V137N, S138Q, S138H, S138N, T140Q, T140H, T140N, S141Q, S141H, S141N, K142N, K142Q, L143I, L143V, T144Q, T144H, T144N, R145H, R145Q, A146Q, A146H, A146N, E147Q, E147H, E147N, T148Q, T148H, T148N, V149Q, V149H, V149N, P151A, P151S, D152N, D152Q, V153Q, V153H, V153N, D154N, D154Q, Y155H, Y155I, V156Q, V156H, V156N, S158Q, S158H, S158N, T159Q, T159H, T159N, E160Q, E160H, E160N, A161Q, A161H, A161N, E162Q, E162H, E162N, T163Q, T163H, T163N, I164Q, I164H, I164N, L165I, L165V, L165Q, L165H, D166N, D166Q, I168Q, I168H, I168N, T169Q, T169H, T169N, S171Q, S171H, S171N, T172Q, T172H, T172N, S174Q, S174H, S174N, F175I, F175V, F175H, D177N, D177Q, F178I, F178V, F178H, T179Q, T179H, T179N, R180H, R180Q, V181Q, V181H, V181N, V182Q, V182H, V182N, G183Q, G183H, G183N, G184Q, G184H, G184N, E185Q, E185H, E185N, D186N, D186Q, A187Q, A187H, A187N, K188N, K188Q, P189A, P189S, G190Q, G190H, G190N, F192I, F192V, F192IH, P193A, P193S, W194S, W194H, W194I, V196Q, V196H, V196N, V197Q, V197H, V197N, L198I, L198V, L198Q, L198H, N199Q, N199S, G200Q, G200H, G200N, K201N, K201Q, V202Q, V202H, V202N, D203N, D203Q, A204Q, A204H, A204N, F205I, F205V, G207Q, G207H, G207N, G208Q, G208H, G208N, S209Q, S209H, S209N, I210Q, I210H, I210N, V211Q, V211H, V211N, E213Q, E213H, E213N, K214N, K214Q, W215S, W215H, I216Q, I216H, I216N, V217Q, V217H, V217N, T218Q, T218H, T218N, A219Q, A219H, A219N, A220Q, A220H, A220N, V223Q, V223H, V223N, E224Q, E224H, E224N, T225Q, T225H, T225N, G226Q, G226H, G226N, V227Q, V227H, V227N, K228N, K228Q, I229Q, I229H, I229N, T230Q, T230H, T230N, V231Q, V231H, V231N, V232Q, V232H, V232N, A233Q, A233H, A233N, G234Q, G234H, G234N, E235Q, E235H, E235N, I238Q, I238H, I238N, E239Q, E239H, E239N, E240Q, E240H, E240N, T241Q, T241H, T241N, E242Q, E242H, E242N, T244Q, T244H, T244N, E245Q, E245H, E245N, K247N, K247Q, R248H, R248Q, V250Q, V250H, V250N, I251Q, I251H, I251N, R252H, R252Q, I253Q, I253H, I253N, I254Q, I254H, I254N, P255A, P255S, Y259H, Y259I, A261Q, A261H, A261N, A262Q, A262H, A262N, I263Q, I263H, I263N, K265N, K265Q, Y266H, Y266I, D269N, D269Q, I270Q, I270H, I270N, A271Q, A271H, A271N, L272I, L272V, L273I, L273V, E274Q, E274H, E274N, L275I, L275V, D276N, D276Q, E277Q, E277H, E277N, P278A, P278S, L279I, L279V, V280Q, V280H, V280N, L281I, L281V, S283Q, S283H, S283N, Y284H, Y284I, V285Q, V285H, V285N, T286Q, T286H, T286N, P287A, P287S, I288Q, I288H, I288N, I290Q, I290H, I290N, A291Q, A291H, A291N, D292N, D292Q, K293N, K293Q, E294Q, E294H, E294N, Y295H, Y295I, T296Q, T296H, T296N, I298Q, I298H, I298N, F299I, F299V, L300I, L300V, K301N, K301Q, F302I, F302V, G303Q, G303H, G303N, S304Q, S304H, S304N, G305Q, G305H, G305N, Y306H, Y306I, V307Q, V307H, V307N, S308Q, S308H, S308N, G309Q, G309H, G309N, W310S, W310H, G311Q, G311H, G311N, R312H, R312Q, V313Q, V313H, V313N, F314I, F314V, K316N, K316Q, G317Q, G317H, G317N, R318H, R318Q, S319Q, S319H, S319N, A320Q, A320H, A320N, L321I, L321V, V322Q, V322H, V322N, L323I, L323V, Y325H, Y325I, L326I, L326V, R327H, R327Q, V328Q, V328H, V328N, P329A, P329S, L330I, L330V, V331Q, V331H, V331N, D332N, D332Q, R333H, R333Q, A334Q, A334H, A334N, T335Q, T335H, T335N, L337I, L337V, R338H, R338Q, S339Q, S339H, S339N, T340Q, T340H, T340N, K341N, K341Q, F342I, F342V, T343Q, T343H, T343N, I344Q, I344H, I344N, Y345H, Y345I, M348I, M348V, F349I, F349V, A351Q, A351H, A351N, G352Q, G352H, G352N, F353I, F353V, E355Q, E355H, E355N, G356Q, G356H, G356N, G357Q, G357H, G357N, R358H, R358Q, D359N, D359Q, S360Q, S360H, S360N, G363Q, G363H, G363N, D364N, D364Q, S365Q, S365H, S365N, G366Q, G366H, G366N, G367Q, G367H, G367N, P368A, P368S, V370Q, V370H, V370N, T371Q, T371H, T371N, E372Q, E372H, E372N, V373Q, V373H, V373N, E374Q, E374H, E374N, G375Q, G375H, G375N, T376Q, T376H, T376N, S377Q, S377H, S377N, F378I, F378V, L379I, L379V, T380Q, T380H, T380N, G381Q, G381H, G381N, I382Q, I382H, I382N, I383Q, I383H, I383N, S384Q, S384H, S384N, W385S, W385H, G386Q, G386H, G386N, E387Q, E387H, E387N, E388Q, E388H, E388N, A390Q, A390H, A390N, M391I, M391V, K392N, K392Q, G393Q, G393H, G393N, K394N, K394Q, Y395H, Y395I, G396Q, G396H, G396N, I397Q, I397H, I397N, Y398H, Y398I, T399Q, T399H, T399N, K400N, K400Q, V401Q, V401H, V401N, S402Q, S402H, S402N, R403H, R403Q, Y404H, Y404I, V405Q, V405H, V405N, W407S, W407H, I408Q, I408H, I408N, K409N, K409Q, E410Q, E410H, E410N, K411N, K411Q, T412Q, T412H, T412N, K413N, K413Q, L414I, L414V, T415Q, T415H, and T415N of a mature FIX polypeptide set forth in SEQ ID NO: 2. In some examples, the modifications are in an unmodified FIX polypeptide having a sequence of amino acids set forth in SEQ ID NO: 2. Provided herein are modified FIX Super-LEAD polypeptides containing two or more amino acid modifications and exhibiting increased protein stability having a sequence of amino acids set forth in any of SEQ ID NOS: 917-1024. In some examples, the modifications are in a FIX polypeptide, such as a FIX polypeptide having a sequence of amino acids set forth in SEQ ID NO: 892 or 1035. For example, exemplary modified FIX LEAD candidate polypeptides are set forth in any one of SEQ ID NOS: 1927-2034.

In one non-limiting example, a FIX polypeptide can contain a modification at a position corresponding to F1921 of a mature FIX polypeptide set forth in SEQ ID NO: 2, and can contain further amino acid modifications, such as any modification set forth in Table 5. Exemplary super-LEAD FIX polypeptides are set forth in Table 7 with the sequence identifier (SEQ ID NO.) in parenthesis next to each substitution. Resulting super-LEADs can be tested for one or more parameters to assess protein stability (such as, increased resistance to proteases) using any of the assays described herein, such as is described in the Examples.

TABLE 7 Exemplary Modified FIX Super-LEADs to Increase Protein Stability T163H/F192I (917) I164Q/F192I (918) T169H/F192I (919) S171Q/F192I (920) D152N/D154N/F192I (921) S174Q/F192I (922) S174H/F192I (923) T179Q/F192I (924) T179H/F192I (925) T163N/I164N/F192I (926) D166Q/F192I (927) D166N/F192I (928) D186Q/F192I (929) D186N/F192I (930) T148A/D152N/ D154N/F192I (931) F192I/D203Q (932) F192I/D203N (933) D152N/F192I (934) D152Q/F192I (935) T148A/D152N/ F192I (936) D154N/F192I (937) D154Q/F192I (938) T163N/I164N (939) A187N/G190N (940) V196N/V197N (941) T140N/T144N (942) F175I/F178I (943) F192I/W194I (944) T148A/D152N (945) T148A/D152Q (946) T148A/D154N (947) T148A/D154Q (948) D152N/D154N (949) I168N/T169N/S171N/ T172N/S174N (950) T179N/V181N/V182N/ D152N/D154N/T148A (952) T163H/D166Q/F192I (953) T163H/D166N/F192I (954) G183N/G184N (951) T163H/D186Q/F192I (955) T163H/D186N/F192I (956) T163H/F192I/D203Q (957) T163H/F192I/D203N (958) T148A/D152N/D154N/ T148A/D154N/T163H/ I164Q/D166Q/F192I (961) I164Q/D166N/F192I (962) T163H/F192I (959) F192I (960) I164Q/D186Q/F192I (963) I164Q/D186N/F192I (964) I164Q/F192I/D203Q (965) I164Q/F192I/D203N (966) T148A/D152N/D154N/ T148A/D154N/I164Q/ T163N/I164N/D166Q/ T163N/I164N/D166N/ I164Q/F192I (967) F192I (968) F192I (969) F192I (970) T163N/I164N/D186Q/ T163N/I164N/D186N/ T163N/I164N/F192I/ T163N/I164N/F192I/ F192I (971) F192I (972) D203Q (973) D203N (974) T148A/D152N/D154N/ T148A/D154N/T163N/ D166Q/T169H/F192I (977) D166N/T169H/F192I (978) T163N/I164N/F192I (975) I164N/F192I (976) T169H/D186Q/F192I (979) T169H/D186N/F192I (980) T169H/F192I/D203Q (981) T169H/F192I/D203N (982) T148A/D152N/D154N/ T148A/D154N/T169H/ D166Q/S171Q/F192I (985) D166N/S171Q/F192I (986) T169H/F192I (983) F192I (984) S171Q/D186Q/F192I (987) S171Q/D186N/F192I (988) S171Q/F192I/D203Q (989) S171Q/F192I/D203N (990) T148A/D152N/D154N/ T148A/D154N/S171Q/ D166Q/S174Q/F192I (993) D166N/S174Q/F192I (994) S171Q/F192I (991) F192I (992) S174Q/D186Q/F192I (995) S174Q/D186N/F192I (996) S174Q/F192I/D203Q (997) S174Q/F192I/D203N (998) T148A/D152N/D154N/ T148A/D154N/S174Q/ D166Q/S174H/F192I (1001) D166N/S174H/F192I (1002) S174Q/F192I (999) F192I (1000) S174H/D186Q/F192I (1003) S174H/D186N/F192I (1004) S174H/F192I/D203Q (1005) S174H/F192I/D203N (1006) T148A/D152N/D154N/ T148A/D154N/S174H/ D166Q/T179Q/F192I (1009) D166N/T179Q/F192I (1010) S174H/F192I (1007) F192I (1008) T179Q/D186Q/F192I (1011) T179Q/D186N/F192I (1012) T179Q/F192I/D203Q (1013) T179Q/F192I/D203N (1014) T148A/D152N/D154N/ T148A/D154N/T179Q/ D166Q/T179H/F192I (1017) D166N/T179H/F192I (1018) T179Q/F192I (1015) F192I (1016) T179H/D186Q/F192I (1019) T179H/D186N/F192I (1020) T179H/F192I/D203Q (1021) T179H/F192I/D203N (1022) T148A/D152N/D154N/ T148A/D154N/T179H/ T179H/F192I (1023) F192I (1024)

Non-limiting examples of FIX SuperLEAD polypeptides containing two or more amino acid modifications and exhibiting increased resistance to proteolysis can include amino acid replacements at amino acid residues corresponding to T163H/F192I, I164Q/F192I, T169H/F192I, S171Q/F192I, D152N/D154N/F192I, S174Q/F192I, S174H/F192I, T179Q/F192I, T179H/F192I, T163N/I164N/F192I, D166Q/F192I, D166N/F192I, D186Q/F192I, D186N/F192I, T148A/D152N/D154N/F192I, F192I/D203Q, F192I/D203N, D152N/F192I, D152Q/F192I, T148A/D154N/F192I, D154N/F192I, D154Q/F192I, T163N/I164N, A187N/G190N, V196N/V197N, T140N/T144N, F175I/F178I, F192I/W194I, T148A/D152N, T148A/D152Q, T148A/D154N, T148A/D154Q, D152N/D154N, I168N/T169N/S171N/T172N/S174N, T179N/V181N/V182N/G183N/G184N, D152N/D154N/T148A, T163H/D166Q/F192I, T163H/D166N/F192I, T163H/D186Q/F192I, T163H/D186N/F192I, T163H/F192I/D203Q, T163H/F192I/D203N, T148A/D152N/D154N/T163H/F192I, T148A/D154N/T163H/F192I, I164Q/D166Q/F192I, I164Q/D166N/F192I, I164Q/D186Q/F192I, I164Q/D186N/F192I, I164Q/F192I/D203Q, I164Q/F192I/D203N, T148A/D152N/D154N/I164Q/F192I, T148A/D154N/I164Q/F192I, T163N/I164N/D166Q/F192I, T163N/I164N/D166N/F192I, T163N/I164N/D186Q/F192I, T163N/I164N/D186N/F192I, T163N/I164N/F192I/D203Q, T163N/I164N/F192I/D203N, T148A/D152N/D154N/T163N/I164N/F192I, T148A/D154N/T163N/I164N/F192I, D166Q/T169H/F192I, D166N/T169H/F192I, T169H/D186Q/F192I, T169H/D186N/F192I, T169H/F192I/D203Q, T169H/F192I/D203N, T148A/D152N/D154N/T169H/F192I, T148A/D154N/T169H/F192I, D166Q/S171Q/F192I, D166N/S171Q/F192I, S171Q/D186Q/F192I, S171Q/D186N/F192I, S171Q/F192I/D203Q, S171Q/F192I/D203N, T148A/D152N/D154N/S171Q/F192I, T148A/D154N/S171Q/F192I, D166Q/S174Q/F192I, D166N/S174Q/F192I, S174Q/D186Q/F192I, S174Q/D186N/F192I, S174Q/F192I/D203Q, S174Q/F192I/D203N, T148A/D152N/D154N/S174Q/F192I, T148A/D154N/S174Q/F192I, D166Q/S174H/F192I, D166N/S174H/F192I, S174H/D186Q/F192I, S174H/D186N/F192I, S174H/F192I/D203 Q, S174H/F192I/D203N, T148A/D152N/D154N/S174H/F192I, T148A/D154N/S174H/F192I, D166Q/T179Q/F192I, D166N/T179Q/F192I, T179Q/D186Q/F192I, T179Q/D186N/F192I, T179Q/F192I/D203Q, T179Q/F192I/D203N, T148A/D152N/D154N/T179Q/F192I, T148A/D154N/T179Q/F192I, D166Q/T179H/F192I, D166N/T179H/F192I, T179H/D186Q/F192I, T179H/D186N/F192I, T179H/F192I/D203Q, T179H/F192I/D203N, T148A/D152N/D154N/T179H/F192I, and T148A/D154N/T179H/F1921 of a mature FIX polypeptide set forth in SEQ ID NO: 2 or 1035. Exemplary modified FIX SuperLEAD polypeptides containing two or more amino acid modifications and exhibiting increased protease resistance have a sequence of amino acids set forth in any one of SEQ ID NOS: 917-1024 or 1927-2034.

3. Other FIX Modifications

In addition to any one or more amino acid modifications provided herein, a modified FIX polypeptide also can contain one or more other modifications, including those known to those of skill in the art, such as PEGylation, hyperglycosylation, deimmunization and others (see such as U.S. Pat. Nos. 6,277,618, 6,315,995, and 6,531,298 and U.S. Patent Publication Nos. 2004-0102388, 2004-0110675, 2004-0254106, 2005-0100982, and 2006-0040856). Generally, the modification results in increased stability without losing at least one activity, such as blood coagulation activity (i.e. retains at least one activity as defined herein) of an unmodified FIX polypeptide. For example, other further modifications in a FIX polypeptide include one or more additional amino acid modifications and/or one or more chemical modifications. Such modifications include, but are not limited to, those that alter the immunogenicity, glycosylation, activity, or any other known property of a FIX polypeptide. In another example, chemical modifications include post-translational modifications of a protein, such as for example, glycosylation by a carbohydrate moiety; acylation; methylation; phosphorylation; sulfation; prenylation; Vitamin C-dependent modifications such as for example, proline, aspartic acid, lysine hydroxylations and carboxy terminal amidation; Vitamin K-dependent modifications such as for example, carboxylation of glutamic acid residues (i.e. gla residue); and incorporation of selenium to form a selenocysteine. Other protein modifications of a FIX polypeptide include PEGylation. In addition, protein modifications also can include modification to facilitate the detection, purification and assay development of a polypeptide, such as for example, modification of a polypeptide with a Sulfo-NHS-LC-biotin for covalent attachment to a primary amine on a protein, or other similar modification for florescent, non-isotopic or radioactive labels. Exemplary further modifications in a FIX polypeptide are described below. Modified polypeptides that are conjugates and/or labeled also are provided. For example, provided herein are modified polypeptides that are conjugated to a PEG moiety or contain a carbohydrate moiety covalently linked to one or more glycosylation sites on the polypeptide.

In another embodiment, other known properties of a FIX polypeptide can be modified in addition to any one or more amino acid modifications provided herein. Such modifications include, but are not limited to, alteration of the peptidase activity, coagulant activity, esterase activity, protein binding activities (such as FVIII), cofactor binding activities, such as Ca²⁺, phospholipid or cell surface binding activities, and increased resistance to inhibitors, such as heparin and warfarin. Resulting modified FIX polypeptides can be tested for one or more parameters to assess polypeptide properties, such as protein stability (such as, increased resistance to proteases), or polypeptide activities, such as coagulant activity, using any of the assays described herein.

In yet another embodiment, known properties of a FIX polypeptide, as mentioned above, can be modified by generation of chimeric FIX polypeptides, in which all, or portions thereof, of FIX polypeptide domains are replaced by homologous domains of other coagulation factor family members. Such chimeric proteins are known in the art and can be combined with the methods for modification of FIX polypeptides provided herein (International PCT application No. WO 2006/018204 A1, Lin et al. (1990) J. Biol. Chem. 265(1):144-150 and Cheung et al. (1991) J. Biol. Chem. 266(14):8797-880). An exemplary chimeric protein has a sequence of amino acids as set forth in SEQ ID NO: 1035.

a. Immunogenicity

There are many instances where the efficacy of a therapeutic protein is limited by an unwanted immune reaction to the therapeutic protein. An immune response to a therapeutic protein, such as FIX, proceeds via the MHC class II peptide presentation pathway. Here, exogenous proteins are engulfed and processed for presentation in association with MHC class II molecules of the DR, DQ or DP type. MHC class II molecules are expressed by professional antigen presenting cells (APCs), such as macrophages and dendritic cells, amongst others. Engagement of a MHC class II peptide complex by a cognate T-cell receptor on the surface of the T cell, together with the cross binding of certain other co-receptors, such as the CD4 molecule, can induce an activated state within the T cell. Activation leads to the release of cytokines, further activating other lymphocytes such as B cells to produce antibodies or activating T killer cells as a full cellular immune response.

The ability of a peptide (T cell epitope) to bind a given MHC class II molecule for presentation on the surface of an APC is dependent on a number of factors, most notably its primary sequence. This will influence its propensity for proteolytic cleavage and also its affinity for binding within the peptide binding cleft of the MHC class II molecule. The MHC class II/peptide complex on the APC surface presents a binding face to a particular T cell receptor (TCR) able to recognize determinants provided by exposed residues of the peptide and the MHC class II molecule.

Formation of inhibitory antibodies to therapeutic FIX polypeptides is known in the art (Herzog et al. (2004) Semin. Thromb. Hemost. 30(2): 215-226). Hence, the combination modified FIX polypeptides provided herein with modifications to decrease overall immunogenicity of the modified FIX polypeptides can improve the therapeutic properties of the FIX polypeptide. The identification of T cell epitopes can be carried out according to methods known in the art (see such as, U.S. Patent Publication No. 20040254106) and can be used to identify the binding propensity of FIX peptides to an MHC class II molecule.

Further modifications to a modified FIX polypeptide provided herein can include modifications of at least one amino acid residue resulting in a substantial reduction in activity of or elimination of one or more T cell epitopes from the protein, i.e. deimmunization of the polypeptide. One or more amino acid modification at particular positions within any of the MHC class II ligands can result in a deimmunized FIX polypeptide with a reduced immunogenic when administered as a therapeutic to a host, such as for example, a human host.

Exemplary amino acid positions for modification of a T cell epitope, and thereby a deimmunized FIX polypeptide with a reduced immunogenic potential, include amino acid modifications at one or more positions corresponding to any of the following positions: Y1, S3, L6, F9, V10, Q11, G12, N13, L14, E15, R16, E17, C18, M19, E20, E21, K22, S24, F25, E26, E27, A28, R29, E30, V31, F32, E33, T35, F41, W42, K43, Q44, Y45, V46, D47, G48, D49, Q50, C51, E52, S53, N54, L57, G60, C62, K63, D65, I66, Y69, C71, W72, F75, F77, L84, V86, I90, K91, N92, G93, R94, C95, E96, Q97, F98, K100, N101, A103, D104, K106, V107, V108, V108, S110, C111, T112, E113, G114, Y115, R116, L117, A118, N120, Q121, S123, V128, F130, V135, V137, S138, T140, S141, K142, L143, R145, A146, T148, V149, F150, D152, V153, D154, Y155, V156, N157, S158, T159, E160, A161, E162, T163, I164, L165, 1168, F175, F178, T179, R180, V181, V182, G183, G184, E185, D186, A187, K188, G190, F192, W194, Q195, V196, V197, L198, N199, G200, K201, V202, D203, A204, F205, G207, G208, S209, I210, V211, N212, E213, K214, W215, I216, V217, A219, V223, G226, V227, K228, I229, T230, V231, V232, A233, G234, E235, H236, N237, I238, E239, E240, V250, I251, I253, I254, P255, H256, H257, N258, Y259, N260, A261, A262, I263, N264, K265, Y266, N267, H268, D269, I270, A271, L272, L273, E274, L275, D276, E277, P278, L279, V280, L281, S283, Y284, V285, T286, I288, C289, I290, A291, D292, K293, Y295, T296, N297, I298, F299, L300, K301, F302, G303, S304, G305, Y306, V307, S308, W310, G311, V313, F314, H315, K316, G317, R318, S319, A320, L321, V322, L323, Q324, Y325, L326, R327, V328, L330, V331, D332, R333, A334, T335, C336, L337, R338, S339, K341, F342, T343, I344, Y345, N346, N347, M348, F349, C350, A351, G352, F353, H354, E355, G356, G357, R358, D359, S360, C361, V370, V373, E374, G375, S377, F378, L379, T380, G381, I382, I383, S384, W385, E387, E388, A390, M391, K392, G393, Y395, Y398, K400, V401, S402, R403, Y404, V405, N406, W407, I408, K409, E410, K411, K413, of a mature FIX polypeptide set forth in SEQ ID NO: 2 or 1035. Exemplary amino acid modifications that can contribute to reduced immunogenicity of a FIX polypeptide include any one or more amino acid modifications corresponding to any one or more modifications set forth in Table 8 corresponding to amino acid positions of a mature FIX polypeptide set forth in SEQ ID NO: 2 or 1035.

TABLE 8 List of human FIX Modifications for Decreased Immunogenicity Y1A Y1C Y1D Y1E Y1G Y1H Y1K Y1N Y1P Y1Q Y1R Y1S Y1T S3T L6A L6C L6D L6E L6G L6H L6K L6N L6P L6Q L6R L6S L6T L6M F9A F9C F9D F9E F9G F9H F9K F9N F9P F9Q F9R F9S F9T F9I F9M F9W V10A V10C V10D V10E V10G V10H V10K V10N V10P V10Q V10R V10S V10T V10F V10I V10M V10W V10Y Q11A Q11C Q11G Q11P G12D G12E G12G G12H G12K G12N G12P G12Q G12R G12S G12T N13A N13C N13G N13H N13P N13T L14A L14C L14D L14E L14G L14H L14K L14N L14P L14Q L14R L14S L14T L14F L14I L14M L14V L14W L14Y E15D E15H E15P R16A R16C R16G R16P R16T E17A E17C E17G E17P E17T C18D C18E C18G C18H C18K C18N C18P C18Q C18R C18S C18T M19A M19C M19D M19E M19G M19H M19K M19N M19P M19Q M19R M19S M19T M19F M19I M19M M19V M19W M19Y E20A E20C E20G E20P E20T E21A E21C E21G E21P K22H K22P K22T S24H S24P F25A F25C F25D F25E F25G F25H F25K F25N F25P F25Q F25R F25S F25T F25I F25M F25W F25Y E26A E26C E26G E26P E27A E27C E27G E27H E27P E27S E27T A28C A28D A28E A28G A28H A28K A28N A28P A28Q A28R A28S A28T R29A R29C R29G R29P E30D E30H E30P V31A V31C V31D V31E V31G V31H V31K V31N V31P V31Q V31R V31S V31T V31F V31I V31W V31Y F32A F32C F32D F32E F32G F32H F32K F32N F32P F32Q F32R F32S F32T E33H E33N E33P E33Q E33S E33T T35A T35C T35G T35P F41A F41C F41D F41E F41G F41H F41K F41N F41P F41Q F41R F41S F41T F41M F41W F41Y W42A W42C W42D W42E W42G W42H W42K W42N W42P W42Q W42R W42S W42T K43A K43C K43G K43P Q44P Q44T Q44 Y45A Y45C Y45D Y45E Y45G Y45H Y45K Y45N Y45P Y45Q Y45R Y45S Y45T V46A V46C V46D V46E V46G V46H V46K V46N V46P V46Q V46R V46S V46T V46F V46I V46M V46W V46Y D47A D47C D47G D47H D47P D47T G48D G48E G48P G48T D49H D49P D49Q D49T Q50A Q50C Q50D Q50G Q50H Q50P Q50T C51D C51E C51G C51H C51K C51N C51P C51Q C51R C51S C51T E52P E52T S53A S53C S53G S53H S53P S53T N54H N54P N54T L57A L57C L57D L57E L57G L57H L57K L57N L57P L57Q L57R L57S L57T L57F L57I L57M L57W L57Y G60C G60D G60H G60P G60T C62D C62H C62P K63T D65H D65T I66A I66C I66D I66E I66G I66H I66K I66N I66P I66Q I66R I66S I66T I66M I66W I66Y Y69A Y69C Y69D Y69E Y69G Y69H Y69K Y69N Y69P Y69Q Y69R Y69S Y69T C71H C71P W72A W72C W72D W72E W72G W72H W72K W72N W72P W72Q W72R W72S W72T W72I W72Y F75A F75C F75D F75E F75G F75H F75K F75N F75P F75Q F75R F75S F75T F77A F77C F77D F77E F77G F77H F77K F77N F77P F77Q F77R F77S F77T L84A L84C L84D L84E L84G L84H L84K L84N L84P L84Q L84R L84S L84T L84M L84W L84Y V86A V86C V86D V86E V86G V86H V86K V86N V86P V86Q V86R V86S V86T I90A I90C I90D I90E I90G I90H I90K I90N I90P I90Q I90R I90S I90T I90M I90W K91A K91C K91G K91P N92A N92C N92G N92P N92T G93D G93E G93H G93K G93N G93P G93Q G93R G93S G93T R94A R94C R94G R94P C95D C95E C95G C95H C95K C95N C95P C95Q C95R C95S C95T E96P E96T Q97A Q97C Q97G Q97P F98A F98C F98D F98E F98G F98H F98K F98N F98P F98Q F98R F98S F98T F98M F98W F98Y K100A K100C K100G K100P N101H N101T A103D A103E A103H A103K A103N A103P A103Q A103R A103S A103T D104T K106H K106P K106T V107A V107C V107D V107E V107G V107H V107K V107N V107P V107Q V107R V107S V107T V108A V108C V108D V108E V108G V108H V108K V108N V108P V108Q V108R V108S V108T V108F V108M V108W V108Y S110A S110C S110G S110P C111D C111E C111H C111K C111N C111P C111Q C111R C111S C111T T112A T112C T112G T112P E113D E113H E113P G114D G114E G114H G114K G114N G114P G114Q G114R G114S G114T Y115A Y115C Y115D Y115E Y115G Y115H Y115K Y115N Y115P Y115Q Y115R Y115S Y115T Y115M Y115W R116P R116T L117A L117C L117D L117E L117G L117H L117K L117N L117P L117Q L117R L117S L117T A118D A118E A118H A118K A118N A118P A118Q A118R A118S A118T N120D N120H N120P Q121T S123H S123T V128A V128C V128D V128E V128G V128H V128K V128N V128P V128Q V128R V128S V128T F130A F130C F130D F130E F130G F130H F130K F130N F130P F130Q F130R F130S F130T V135A V135C V135D V135E V135G V135H V135K V135N V135P V135Q V135R V135S V135T V135W V135Y V137A V137C V137D V137E V137G V137H V137K V137N V137P V137Q V137R V137S V137T V137M V137W V137Y S138H S138T T140D T140H S141T K142H K142P L143A L143C L143D L143E L143G L143H L143K L143N L143P L143Q L143R L143S L143T L143F L143I L143M L143V L143W L143Y R145H R145P R145T A146P A146T T148H T148P V149A V149C V149D V149E V149G V149H V149K V149N V149P V149Q V149R V149S V149T V149F V149I V149M V149W V149Y F150A F150C F150D F150E F150G F150H F150K F150N F150P F150Q F150R F150S F150T F150M F150W F150Y D152A D152C D152G D152P D152S D152T V153A V153C V153D V153E V153G V153H V153K V153N V153P V153Q V153R V153S V153T V153F V153I V153M V153W V153Y D154A D154C D154G D154P D154Q D154S Y155A Y155C Y155D Y155E Y155G Y155H Y155K Y155N Y155P Y155Q Y155R Y155S Y155T Y155M Y155V Y155W V156A V156C V156D V156E V156G V156H V156K V156N V156P V156Q V156R V156S V156T V156I V156M V156W V156Y N157A N157C N157G N157H N157P N157Q N157T S158H S158P S158T T159A T159C T159G T159P E160A E160C E160G E160P A161C A161D A161E A161H A161K A161N A161P A161Q A161R A161S A161T E162P E162T T163A T163C T163G T163P I164A I164C I164D I164E I164G I164H I164K I164N I164P I164Q I164R I164S I164T L165A L165C L165D L165E L165G L165H L165K L165N L165P L165Q L165R L165S L165T L165M L165W L165Y I168A I168C I168D I168E I168G I168H I168K I168N I168P I168Q I168R I168S I168T F175A F175C F175D F175E F175G F175H F175K F175N F175P F175Q F175R F175S F175T F178A F178C F178D F178E F178G F178H F178K F178N F178P F178Q F178R F178S F178T F178M F178W F178Y T179A T179C T179G T179P R180A R180C R180D R180G R180H R180P V181A V181C V181D V181E V181G V181H V181K V181N V181P V181Q V181R V181S V181T V181F V181I V181M V181W V181Y V182A V182C V182D V182E V182G V182H V182K V182N V182P V182Q V182R V182S V182T V182F V182I V182M V182W V182Y G183D G183E G183H G183K G183N G183P G183Q G183S G183T G184D G184E G184H G184K G184N G184P G184Q G184R G184S G184T E185A E185C E185G E185H E185P E185T D186A D186C D186G D186H D186P D186T A187C A187D A187E A187G A187H A187K A187N A187P A187Q A187R A187S A187T K188A K188C K188G K188H K188P K188T G190D G190E G190H G190K G190N G190P G190Q G190R G190S G190T F192A F192C F192D F192E F192G F192H F192K F192N F192P F192Q F192R F192S F192T F192W F192Y W194A W194C W194D W194E W194G W194H W194K W194N W194P W194Q W194R W194S W194T Q195H Q195P Q195T V196A V196C V196D V196E V196G V196H V196K V196N V196P V196Q V196R V196S V196T V196F V196I V196M V196W V196Y V197A V197C V197D V197E V197G V197H V197K V197N V197P V197Q V197R V197S V197T V197F V197I V197M V197W V197Y L198A L198C L198D L198E L198G L198H L198K L198N L198P L198Q L198R L198S L198T L198I L198Y N199A N199C N199G N199H N199P N199S N199T G200P G200T K201A K201C K201D K201E K201G K201H K201N K201P K201Q K201S K201T V202A V202C V202D V202E V202G V202H V202K V202N V202P V202Q V202R V202S V202T V202F V202I V202M V202W V202Y D203A D203C D203G D203P D203T A204C A204D A204E A204G A204H A204K A204N A204P A204Q A204R A204S A204T F205A F205C F205D F205E F205G F205H F205K F205N F205P F205Q F205R F205S F205T F205M F205V F205W F205Y G207H G207P G208C G208D G208E G208H G208K G208N G208P G208Q G208R G208S G208T S209A S209C S209G S209P I210A I210C I210D I210E I210G I210H I210K I210N I210P I210Q I210R I210S I210T I210F I210W I210Y V211A V211C V211D V211E V211G V211H V211K V211N V211P V211Q V211R V211S V211T V211F V211I V211M V211W N212A N212C N212G N212P E213H E213P E213S E213T K214T W215A W215C W215D W215E W215G W215H W215K W215N W215P W215Q W215R W215S W215T I216A I216C I216D I216E I216G I216H I216K I216N I216P 1216Q I216R I216S I216T V217A V217C V217D V217E V217G V217H V217K V217N V217P V217Q V217R V217S V217T V217I V217Y A219H A219P A219T V223A V223C V223D V223E V223G V223H V223K V223N V223P V223Q V223R V223S V223T V223M V223W V223Y G226P V227A V227C V227D V227E V227G V227H V227K V227N V227P V227Q V227R V227S V227T V227F V227I V227M V227W V227Y K228A K228C K228G K228H K228P I229A I229C I229D I229E I229G I229H I229K I229N I229P I229Q I229R I229S I229T I229M I229W I229Y T230A T230C T230G T230P V231A V231C V231D V231E V231G V231H V231K V231N V231P V231Q V231R V231S V231T V232A V232C V232D V232E V232G V232H V232K V232N V232P V232Q V232R V232S V232T V232F V232I V232M V232W V232Y A233C A233D A233E A233G A233H A233K A233N A233P A233Q A233R A233S A233T A233V G234D G234E G234H G234K G234N G234P G234Q G234R G234S G234T E235H E235N E235P E235Q E235S E235T H236A H236C H236G H236P N237A N237C N237G N237P N237T I238A I238C I238D I238E I238G I238H I238K I238N I238P I238Q I238R I238S I238T E239A E239C E239G E239P E240H E240T V250A V250C V250D V250E V250G V250H V250K V250N V250P V250Q V250R V250S V250T V250M V250W V250Y I251A I251C I251D I251E I251G I251H I251K I251N I251P I251Q I251R I251S I251T I253A I253C I253D I253E I253G I253H I253K I253N I253P I253Q I253R I253S I253T I253M I253W I253Y I254A I254C I254D I254E I254G I254H I254K I254N I254P I254Q I254R I254S I254T P255H H256P H256T H257A H257C H257G H257P N258P N258T Y259A Y259C Y259D Y259E Y259G Y259H Y259K Y259N Y259P Y259Q Y259R Y259S Y259T Y259M Y259W N260A N260C N260G N260P A261D A261E A261H A261K A261N A261P A261Q A261R A261S A261T A262C A262D A262E A262G A262H A262K A262N A262P A262Q A262R A262S A262T I263A I263C I263D I263E I263G I263H I263K I263N I263P I263Q I263R I263S I263T I263M I263V I263W I263Y N264A N264C N264D N264G N264H N264P K265A K265C K265G K265H K265P Y266A Y266C Y266D Y266E Y266G Y266H Y266K Y266N Y266P Y266Q Y266R Y266S Y266T Y266M Y266W N267A N267C N267G N267H N267P N267T H268P D269A D269C D269E D269G D269H D269N D269P D269Q D269S D269T I270A I270C I270D I270E I270G I270H I270K I270N I270P I270Q I270R I270S I270T I270M I270W A271C A271D A271E A271G A271H A271K A271N A271P A271Q A271R A271S A271T L272A L272C L272D L272E L272G L272H L272K L272N L272P L272Q L272R L272S L272T L272F L273A L273C L273D L273E L273G L273H L273K L273N L273P L273Q L273R L273S L273T L273F L273I L273M L273V L273W L273Y E274A E274C E274G E274P E274T L275A L275C L275D L275E L275G L275H L275K L275N L275P L275Q L275R L275S L275T L275W L275Y D276P D276S D276T E277A E277C E277G E277P P278T L279A L279C L279D L279E L279G L279H L279K L279N L279P L279Q L279R L279S L279T L279I L279Y V280A V280C V280D V280E V280G V280H V280K V280N V280P V280Q V280R V280S V280T V280F V280I V280W V280Y L281A L281C L281D L281E L281G L281H L281K L281N L281P L281Q L281R L281S L281T L281F L281I L281V L281W L281Y S283A S283C S283G S283P Y284A Y284C Y284D Y284E Y284G Y284H Y284K Y284N Y284P Y284Q Y284R Y284S Y284T Y284M V285A V285C V285D V285E V285G V285H V285K V285N V285P V285Q V285R V285S V285T V285M V285W V285Y T286A T286C T286G T286P I288A I288C I288D I288E I288G I288H I288K I288N I288P I288Q I288R I288S I288T C289D C289H C289P I290A I290C I290D I290E I290G I290H I290K I290N I290P I290Q I290R I290S I290T I290Y A291D A291E A291H A291K A291N A291P A291Q A291R A291S A291T D292A D292C D292G D292P D292T K293H K293P K293T Y295A Y295C Y295D Y295E Y295G Y295H Y295K Y295N Y295P Y295Q Y295R Y295S Y295T Y295W T296A T296C T296G T296P N297A N297C N297G N297P I298A I298C I298D I298E I298G I298H I298K I298N I298P I298Q I298R I298S I298T F299A F299C F299D F299E F299G F299H F299K F299N F299P F299Q F299R F299S F299T L300A L300C L300D L300E L300G L300H L300K L300N L300P L300Q L300R L300S L300T L300F L300I L300M L300V L300W L300Y K301A K301C K301G K301P K301T F302A F302C F302D F302E F302G F302H F302K F302N F302P F302Q F302R F302S F302T G303H G303P G303T S304A S304C S304G S304P S304T G305D G305E G305H G305N G305P G305Q G305S G305T Y306A Y306C Y306D Y306E Y306G Y306H Y306K Y306N Y306P Y306Q Y306R Y306S Y306T V307A V307C V307D V307E V307G V307H V307K V307N V307P V307Q V307R V307S V307T S308P S308T W310A W310C W310D W310E W310G W310H W310K W310N W310P W310Q W310R W310S W310T G311H V313A V313C V313D V313E V313G V313H V313K V313N V313P V313Q V313R V313S V313T F314A F314C F314D F314E F314G F314H F314K F314N F314P F314Q F314R F314S F314T F314M F314W F314Y H315A H315C H315G H315P K316A K316C K316G K316P G317C G317D G317E G317H G317K G317N G317P G317Q G317R G317S G317T R318A R318C R318G R318P S319D S319H S319N S319P S319Q A320C A320D A320E A320G A320H A320K A320N A320P A320Q A320R A320S A320T L321A L321C L321D L321E L321G L321H L321K L321N L321P L321Q L321R L321S L321T V322A V322C V322D V322E V322G V322H V322K V322N V322P V322Q V322R V322S V322T V322W V322Y L323A L323C L323D L323E L323G L323H L323K L323N L323P L323Q L323R L323S L323T L323F L323I L323M L323V L323W L323Y Q324A Q324C Q324G Q324P Y325A Y325C Y325D Y325E Y325G Y325H Y325K Y325N Y325P Y325Q Y325R Y325S Y325T Y325W L326A L326C L326D L326E L326G L326H L326K L326N L326P L326Q L326R L326S L326T L326F L326I L326M L326V L326W L326Y R327A R327C R327G R327H R327P V328A V328C V328D V328E V328G V328H V328K V328N V328P V328Q V328R V328S V328T V328F V328I V328M V328W V328Y L330A L330C L330D L330E L330G L330H L330K L330N L330P L330Q L330R L330S L330T L330F L330I L330V L330W L330Y V331A V331C V331D V331E V331G V331H V331K V331N V331P V331Q V331R V331S V331T V331F V331I V331M V331W V331Y D332A D332C D332G D332P R333A R333C R333D R333E R333G R333H R333N R333P R333Q R333R R333S R333T A334C A334D A334E A334G A334H A334K A334N A334P A334Q A334R A334S A334T T335A T335C T335G T335P C336D C336E C336H C336K C336N C336P C336Q C336R C336S C336T L337A L337C L337D L337E L337G L337H L337K L337N L337P L337Q L337R L337S L337T R338A R338C R338G R338P S339P S339T K341A K341C K341G K341P F342A F342C F342D F342E F342G F342H F342K F342N F342P F342Q F342R F342S F342T F342M F342W T343A T343C T343G T343P I344A I344C I344D I344E I344G I344H I344K I344N I344P I344Q I344R I344S I344T Y345A Y345C Y345D Y345E Y345G Y345H Y345K Y345N Y345P Y345Q Y345R Y345S Y345T Y345M Y345W N346A N346C N346G N346P N347H N347P M348A M348C M348D M348E M348G M348H M348K M348N M348P M348Q M348R M348S M348T F349A F349C F349D F349E F349G F349H F349K F349N F349P F349Q F349R F349S F349T F349I F349M F349W F349Y C350D C350H C350P C350T A351E A351H A351N A351P A351Q A351R A351S A351T G352A G352C G352P F353A F353C F353D F353E F353G F353H F353K F353N F353P F353Q F353R F353S F353T F353I F353M F353W H354A H354C H354G H354P E355A E355C E355D E355G E355H E355K E355N E355P E355Q E355S E355T G356D G356E G356H G356K G356N G356P G356Q G356R G356S G356T G357D G357E G357H G357K G357N G357P G357Q G357R G357S G357T R358D R358E R358H R358K R358N R358P R358Q R358R R358S R358T D359A D359C D359G D359P D359Q D359S D359T S360A S360C S360G S360P C361D C361E C361H C361K C361N C361P C361Q C361R C361S C361T V370A V370C V370D V370E V370G V370H V370K V370N V370P V370Q V370R V370S V370T V370W V370Y V373A V373C V373D V373E V373G V373H V373K V373N V373P V373Q V373R V373S V373T V373F V373I V373M V373W E374A E374C E374G E374P G375H S377A S377C S377G S377P F378A F378C F378D F378E F378G F378H F378K F378N F378P F378Q F378R F378S F378T F378W L379A L379C L379D L379E L379G L379H L379K L379N L379P L379Q L379R L379S L379T L379I L379M L379W L379Y T380A T380C T380G T380P G381D G381E G381H G381K G381N G381P G381Q G381R G381S G381T I382A I382C I382D I382E I382G I382H I382K I382N I382P I382Q I382R I382S I382T I382M I382W I382Y I383A I383C I383D I383E I383G I383H I383K I383N I383P I383Q I383R I383S I383T S384A S384C S384G S384P W385A W385C W385D W385E W385G W385H W385K W385N W385P W385Q W385R W385S W385T W385M E387A E387C E387G E387H E387P E387T E388H E388N E388P E388Q E388T A390C A390D A390E A390G A390H A390K A390N A390P A390Q A390R A390S M391A M391C M391D M391E M391G M391H M391K M391N M391P M391Q M391R M391S M391T M391F M391I M391W M391Y K392A K392C K392G K392P G393C G393D G393E G393H G393K G393N G393P G393Q G393R G393S G393T Y395A Y395C Y395D Y395E Y395G Y395H Y395K Y395N Y395P Y395Q Y395R Y395S Y395T Y398A Y398C Y398D Y398E Y398G Y398H Y398K Y398N Y398P Y398Q Y398R Y398S Y398T K400H V401A V401C V401D V401E V401G V401H V401K V401N V401P V401Q V401R V401S V401T V401F V401I V401M V401W V401Y S402A S402C S402G S402P R403A R403C R403G R403P R403T Y404A Y404C Y404D Y404E Y404G Y404H Y404K Y404N Y404P Y404Q Y404R Y404S Y404T V405A V405C V405D V405E V405G V405H V405K V405N V405P V405Q V405R V405S V405T V405W V405Y N406F N406H N406I N406L N406P N406W N406Y W407D W407E W407F W407H W407I W407K W407N W407P W407Q W407R W407S W407T W407Y I408D I408E I408H I408K I408N I408P I408Q I408R I408S I408T K409F K409H K409I K409P K409T K409V K409W K409Y E410H K411A K411C K411G K411I K411P K411T K411V K411W K411Y K413T

b. Glycosylation

Many proteins with therapeutic activity contain one or more glycosylation sites, such as, amino acid sequences that are glycosylated by a eukaryotic cell. There have been various reports of attempts to increase the degree of glycosylation of therapeutic proteins in order to achieve 1) reduced immunogenicity; 2) less frequent administration of the protein; 3) increased protein stability such as increased serum half-life; and 4) reduction in adverse side effects such as inflammation. The glycosylation site(s) provides a site for attachment of a carbohydrate moiety on the subject polypeptide, such that when the subject polypeptide is produced in a eukaryotic cell capable of glycosylation, the subject polypeptide is glycosylated. The further glycosylation of a FIX polypeptide confers one or more advantages including increased serum half-life; reduced immunogenicity; increased functional in vivo half-life; reduced degradation by gastrointestinal tract conditions such as gastrointestinal tract proteases; and increased rate of absorption by gut epithelial cells. An increased rate of absorption by gut epithelial cells and reduced degradation by gastrointestinal tract conditions is important for enteral (such as oral) formulations of a FIX polypeptide.

Glycosylation of proteins results in the formation of glycoproteins due to the covalent attachment of oligosaccharides to a polypeptide. The carbohydrate modifications found in glycoproteins are linked to the protein component through either O-glycosidic or N-glycosidic bonds. The predominant carbohydrate attachment in glycoproteins of mammalian cells is via N-glycosidic linkage. The N-glycosidic linkage is through the amide group of asparagines. The site of carbohydrate attachment to N-linked glycoproteins is found within a consensus sequence of amino acids, N-X-S/T, where X is any amino acid except proline. In N-linked glycosylation, the carbohydrate directly attached to the protein is GlcNAc. Since glycosylation is known to be highly host cell-dependent, the sugar chains associated with N-linked glycosylation of a protein can differ (Kagawa et al., (1988) Journal of Biological Chemistry 263:17508-17515). The β-glycosidic linkage is to the hydroxyl of serine, threonine or hydroxylysine. In Ser- and Thr-type O-linked glycoproteins, the carbohydrate directly attached to the protein is GalNAc. A number of O-linked glycosylation sites are known in the art and have been reported in the literature, see such as Ten Hagen et al. (1999) Journal of Biological Chemistry, 274:27867-74; Hanisch et al. (2001) Glycobiology, 11:731-740; and Ten Hagen et al., (2003) Glycobiology, 13:1R-16R.

Modified FIX polypeptides provided herein can further be glycosylated (i.e. hyperglycosylated) as compared to an unmodified FIX polypeptide due to 1) a carbohydrate moiety covalently linked to at least one non-native glycosylation site not found in the unmodified FIX polypeptide or 2) a carbohydrate moiety covalently linked to at least one native glycosylation site found but not glycosylated in the unmodified FIX polypeptide. A hyperglycosylated FIX polypeptide can include O-linked glycosylation, N-linked glycosylation, and/or a combination thereof. In some examples, a hyperglycosylated FIX polypeptide can include 1, 2, 3, 4 or 5 carbohydrate moieties, each linked to different glycosylation sites. The glycosylation site can be a native glycosylation site. In other examples, the hyperglycosylated polypeptide can be glycosylated at a single non-native glycosylation site. In still other examples, the hyperglycosylated polypeptide can be glycosylated at more than one non-native glycosylation site, such as, the hyperglycosylated FIX polypeptide can be glycosylated at 2, 3 or 4 non-native glycosylation sites.

In some instances, a hyperglycosylated FIX polypeptide is glycosylated at a native glycosylation site. For example, FIX, such as for example human FIX having an amino acid sequence set forth in SEQ ID NO: 2, contains N-linked glycosylation sites at N157 and N167 and O-linked glycosylation sites at S53, S61, T159, T169, T172, and T179. The FIX polypeptide can be glycosylated at a single native glycosylation site, or at more than one native glycosylation site, such as, at 2, 3 or 4 native glycosylation sites. A hyperglycosylated FIX polypeptide also can be glycosylated at a native glycosylation site and a non-native glycosylation site. A hyperglycosylated FIX polypeptide also can be glycosylated at multiple native and non-native glycosylation sites.

Modified FIX polypeptides provided herein can have at least one additional carbohydrate moiety not found in the unmodified FIX polypeptide when each is synthesized in a eukaryotic cell that is capable of N- and/or O-linked protein glycosylation. Thus, e.g., compared to an unmodified FIX polypeptide, a hyperglycosylated modified FIX polypeptide can have at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, or more additional carbohydrate moieties. For example, where an unmodified FIX polypeptide has one covalently linked carbohydrate moiety, a hyperglycosylated FIX polypeptide can have 2, 3, 4, 5, 6, 7, 8, 9, 10, or more covalently linked carbohydrate moieties. In some examples, a hyperglycosylated FIX polypeptide of a modified FIX polypeptide provided herein, lacks a carbohydrate moiety covalently linked to a non-native glycosylation site, and has instead at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, or more additional carbohydrate moieties attached to native glycosylation sites. In other examples, a hyperglycosylated FIX polypeptide lacks a carbohydrate moiety covalently linked to a native glycosylation site, and has instead at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, or more carbohydrate moieties attached to non-native glycosylation sites. In some examples, the compositions of the attached sugars can be modified, such as by increasing or decreasing sialic acid content of the attach sugar moieties.

Whether a subject FIX polypeptide has N-linked and/or O-linked glycosylation is readily determined using standard techniques, see such as, “Techniques in Glycobiology” R. Townsend and A. Hotchkiss, eds. (1997) Marcel Dekker; and “Glycoanalysis Protocols (Methods in Molecular Biology, Vol. 76)” E. Hounsell, ed. (1998) Humana Press. The change in electrophoretic mobility of a protein before and after treatment with chemical or enzymatic deglycosylation (such as, using endoglycosidases and/or exoglycosidases) is routinely used to determine the glycosylation status of a protein. Enzymatic deglycosylation can be carried out using any of a variety of enzymes, including, but not limited to, peptide-N4-(N-acetyl-β-D-glycosaminyl) asparagine amidase (PNGase F); endoglycosidase F1, endoglycosidase F2 and endoglycosidase F3, α(2→3,6,8,9) neuraminidase. For example, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis of the protein, either pre-treated with PNGaseF or untreated with PNGaseF, is conducted. A marked decrease in band width and change in migration position after treatment with PNGaseF is considered diagnostic of N-linked glycosylation. The carbohydrate content of a glycosylated protein also can be detected using lectin analysis of protein blots (such as, proteins separated by SDS-PAGE and transferred to a support, such as a nylon membrane). Lectins, carbohydrate binding proteins from various plant tissues, have high affinity and narrow specificity for a wide range of defined sugar epitopes found on glycoprotein glycans (Cummings (1994) Methods in Enzymol. 230:66-86). Lectins can be detectably labeled (either directly or indirectly), allowing detection of binding of lectins to carbohydrates on glycosylated proteins. For example, when conjugated with biotin or digoxigenin, a lectin bound to a glycosylated protein can be easily identified on membrane blots through a reaction utilizing avidin or anti-digoxigenin antibodies conjugated with an enzyme such as alkaline phosphatase, β-galactosidase, luciferase or horse radish peroxidase, to yield a detectable product. Screening with a panel of lectins with well-defined specificity provides considerable information about a glycoprotein's carbohydrate complement.

Exemplary amino acid positions contemplated herein for modification of a glycosylation site, for attachment of a carbohydrate moiety, include positions corresponding to positions N157 or N167 of a mature FIX polypeptide set forth in SEQ ID NO: 2. Amino acid replacement or replacements can correspond to any of the following positions: N157 or N167 of mature FIX. In a particular embodiment, the amino acid replacement or replacements contributing to hyperglycosylation of modified FIX polypeptides is (are) replacement of amino acids by asparagines (N) or threonine (T). Thus, provided herein are modified FIX polypeptides containing a further modification corresponding to any one or more of N157 or N167 of a mature FIX polypeptide set forth in SEQ ID NO: 2.

c. Additional Modifications

Additional modifications of polypeptides provided herein include chemical derivatization of polypeptides, including but not limited to, acetylation and carboxylation; changes in amino acid sequence that make the protein susceptible to PEGylation or other modification or that alter properties of the FIX polypeptide. Related moieties for modifying FIX polypeptides also are contemplated, including, but not limited to copolymers of polyethylene glycol and polypropylene glycol, carboxymethylcellulose, dextran, polyvinyl alcohol, polyvinylpyrrolidine or polyproline (Abuchowski et al. (1981); Newmark et al. (1982); and Katre et al. (1987)). A modified FIX polypeptide provided herein can be modified with one or more polyethylene glycol moieties (PEGylated). Activated PEG derivatives can be used to interact directly with the FIX polypeptides, and include active esters of carboxylic acid or carbonate derivatives, particularly those in which the leaving groups are N-hydroxysuccinimide, p-nitrophenol, imidazole or 1-hydroxy-2-nitrobenzene-4-sulfonate. PEG derivatives containing maleimido or haloacetyl groups can be used for the modification of sulfhydryl groups, and PEG reagents containing hydrazine or hydrazide groups can be used to modify aldehydes generated by periodate oxidation of carbohydrate groups. In some instances, a modified FIX polypeptide provided herein can contain one or more non-naturally occurring pegylation sites that are engineered to provide PEG-derivatized polypeptides with reduced serum clearance (U.S. Published Patent Application No: 2006-0040856).

Also contemplated are modified FIX polypeptides sequences that have phosphorylated amino acid residues, such as phosphotyrosine, phosphoserine or phosphothreonine.

Other suitable additional modifications of a modified FIX polypeptide provided herein are polypeptides that have been modified using standard chemical techniques and/or recombinant nucleic acid method as to increase their resistance to proteolytic degradation, to optimize solubility properties and/or to render them more suitable as a therapeutic agent. For example, the backbone of the peptide can be cyclized to enhance stability (see such as, Friedler et al. (2000) J. Biol. Chem. 275:23783-23789). Analogs can be used that include residues other than naturally occurring L-amino acids, such as, D-amino acids or non-naturally occurring synthetic amino acids.

Modifications of FIX polypeptides provided herein also can be combined with modifications to improve post-translational processing of the FIX polypeptides. For example, FIX polypeptides can be modified to improve proteolytic cleavage of the signal or propeptides sequences (U.S. Pat. Application No. 2004-0102388), and/or to improve post-translational modifications such as carboxylation, phosphorylation, sulfation, and/or glycosylation, as discussed above. An exemplary modification that improves propeptide cleavage includes, modification of Y1, in particular Y1A (Meulien et al. (1990) Protein. Eng. 3(7): 629-633 and U.S. Pat. Nos. 4,770,999 and 5,521,070).

Modifications of FIX polypeptides provided herein also can be combined with amino acid modifications to further improve stability, binding properties and serum half-life of the FIX polypeptides. A non-limiting example of such modification includes replacement of all or part of the FIX activation peptide (amino acid residues A146 through R180 of a mature FIX polypeptide, SEQ ID NO: 2) with an activation peptide of another vitamin K-dependent polypeptide, such as FVII, FX, or protein C. Another non-limiting example of such modification includes replacement of all or part of the gla domain (amino acid residues Y1 through V46 of a mature FIX polypeptide, SEQ ID NO: 2) with a gla domain of another vitamin K-dependent polypeptide, such as FVII, FX, or protein C. Such modifications and generation of chimeric proteins are described in, for example, published International PCT application No. WO 2006/018204 A1, Lin et al. (1990) J. Biol. Chem. 265(1):144-150 and Cheung et al. (1991) J. Biol. Chem. 266(14):8797-880. In another example, amino acid residues in FIX polypeptides that are involved in binding to collagen, in particular collagen IV in the liver, can be modified to increase circulating levels of the FIX polypeptides in the blood. For example, K5 and V 10 in the γ-carboxyglutamic acid (gla) domain can be modified, such as K5A and/or V10K (Cheung et al. (1992) J. Biol. Chem. 267(29): 20529-20531, Gui et al. (2002) Blood 100(1): 153-158, and Schuettrumpf et al. (2005) Blood 105(6): 2316-2323). In yet another example modified FIX polypeptide can contain modifications to increase resistance to inhibition by heparin. One such modification is described in, for example, U.S. Pat. Application No. 2004-0110675.

Additional modifications that alter properties or activities of FIX polypeptides, such as, peptidase activity, coagulant activity, esterase activity, protein binding activities (such as to FVIII, FX, or FXI), cofactor binding activities, such as Ca2+, phospholipid or cell surface binding activities, and increased resistance to inhibitors, such as heparin and warfarin, are known in the art and can be combined with the modifications provided herein. Exemplary modifications of the peptidase activity include replacement of amino acid residues of the catalytic domain, H221, D269, S365 (U.S. Pat. No. 6,315,995) or replacement of 8338 to enhance clotting activity (U.S. Pat. No. 6,531,298 and Chang et al. (1998) J. Biol. Chem. 273(20): 12089-12094). Peptidase activity also can be altered by modifying substrate binding sites or cofactor sites. For example, modifications of K316 can alter binding of factor X to modified FIX polypeptides (Kolkman and Mertens (2000) Biochem. J. 350: 701-707). Exemplary modifications of FIX polypeptides with altered Ca²⁺ binding include replacement of residues in the EGF-like domains, such as, but not limited to, G60S, or replacement of the EGF-1 domain of FIC with that of FVII (Chang et al. (1995) Thromb and Haemost. Abst 73:1202). Exemplary modifications of FIX polypeptides that alter FVIIIa-dependent FIXa activity include mutations in the α-helical regions 333-339 and 301-333, which interact with FVIIIa. One or more properties of a FIX polypeptide may be altered as a result of a modification or combination of modifications. For example, modification of Ca²⁺ binding may lead to a change in coagulation activity.

F. PRODUCTION OF FIX POLYPEPTIDES

1. Expression Systems

FIX polypeptides (modified and unmodified) can be produced by any methods known in the art for protein production, including the introduction of nucleic acid molecules encoding FIX into a host cell, host animal and expression from nucleic acid molecules encoding FIX in vitro. Expression hosts include E. coli, yeast, plants, insect cells, mammalian cells, including human cell lines and transgenic animals. Expression hosts can differ in their protein production levels as well as the types of post-translational modifications that are present on the expressed proteins. The choice of expression host can be made based on these and other factors, such as regulatory and safety considerations, production costs and the need and methods for purification.

Expression in eukaryotic hosts can include expression in yeasts such as Saccharomyces cerevisiae and Pichia Pastoria, insect cells such as Drosophila cells and lepidopteran cells, plants and plant cells such as tobacco, corn, rice, algae and lemna. Eukaryotic cells for expression also include mammalian cells lines such as Chinese hamster ovary (CHO) cells. Eukaryotic expression hosts also include production in transgenic animals, for example, including production in serum, milk and eggs. Transgenic animals for the production of wild-type FIX polypeptides are known in the art (U.S. Patent Publication Nos. 2002-0166130 and 2004-0133930) and can be adapted for production of modified FIX polypeptides provided herein.

Many expression vectors are available for the expression of FIX. The choice of expression vector is influenced by the choice of host expression system. Such selection is well within the level of skill of the skilled artisan. In general, expression vectors can include transcriptional promoters and optionally enhancers, translational signals, and transcriptional and translational termination signals. Expression vectors that are used for stable transformation typically have a selectable marker which allows selection and maintenance of the transformed cells. In some cases, an origin of replication can be used to amplify the copy number of the vectors in the cells.

Methods of production of FIX polypeptides can include coexpression of one or more additional heterologous polypeptides that can aid in the generation of the FIX polypeptides. For example, such polypeptides can contribute to the post-translation processing of the FIX polypeptides. Exemplary polypeptides include, but are not limited to, peptidases that help cleave FIX precursor sequences, such as the propeptide sequence, and enzymes that participate in the modification of the FIX polypeptide, such as by glycosylation, hydroxylation, carboxylation or phosphorylation, for example. An exemplary peptidase that can be coexpressed with FIX is PACE/furin (or PACE-SOL), which aids in the cleavage of the FIX propeptide sequence (Harrison et al. (1998) Semin Hematol. 35(2 Suppl 2): 4-10). An exemplary protein that aids in the carboxylation of the FIX polypeptide is the warfarin-sensitive enzyme vitamin K 2,3-epoxide reductase (VKOR), which produces reduced vitamin K for utilization as a cofactor by the vitamin K-dependent γ-carboxylase (Wajih et al., J. Biol. Chem. 280(36)31603-31607). A subunit of this enzyme, VKORC1, can be coexpressed with the modified FIX polypeptide to increase the γ-carboxylation The one or more additional polypeptides can be expressed from the same expression vector as the FIX polypeptide or from a different vector.

a. Prokaryotic Expression

Prokaryotes, especially E. coli, provide a system for producing large amounts of FIX (see, for example, Platis et al (2003) Protein Exp. Purif. 31(2): 222-30; and Khalizzadeh et al. (2004) J. Ind. Microbiol. Biotechnol. 31(2): 63-69). Transformation of E. coli is a simple and rapid technique well known to those of skill in the art. Expression vectors for E. coli can contain inducible promoters that are useful for inducing high levels of protein expression and for expressing proteins that exhibit some toxicity to the host cells. Examples of inducible promoters include the lac promoter, the trp promoter, the hybrid tac promoter, the T7 and SP6 RNA promoters and the temperature regulated λP_(L) promoter.

FIX can be expressed in the cytoplasmic environment of E. coli. The cytoplasm is a reducing environment and for some molecules, this can result in the formation of insoluble inclusion bodies. Reducing agents such as dithiothreitol and β-mercaptoethanol and denaturants (such as, such as guanidine-HCl and urea) can be used to resolubilize the proteins. An alternative approach is the expression of FIX in the periplasmic space of bacteria which provides an oxidizing environment and chaperonin-like and disulfide isomerases leading to the production of soluble protein. Typically, a leader sequence is fused to the protein to be expressed which directs the protein to the periplasm. The leader is then removed by signal peptidases inside the periplasm. Examples of periplasmic-targeting leader sequences include the pelB leader from the pectate lyase gene and the leader derived from the alkaline phosphatase gene. In some cases, periplasmic expression allows leakage of the expressed protein into the culture medium. The secretion of proteins allows quick and simple purification from the culture supernatant. Proteins that are not secreted can be obtained from the periplasm by osmotic lysis. Similar to cytoplasmic expression, in some cases proteins can become insoluble and denaturants and reducing agents can be used to facilitate solubilization and refolding. Temperature of induction and growth also can influence expression levels and solubility. Typically, temperatures between 25° C. and 37° C. are used. Mutations also can be used to increase solubility of expressed proteins. Typically, bacteria produce aglycosylated proteins. Thus, if proteins require glycosylation for function, glycosylation can be added in vitro after purification from host cells.

b. Yeast

Yeasts such as Saccharomyces cerevisiae, Schizosaccharomyces pombe, Yarrowia lipolytica, Kluyveromyces lactis, and Pichia pastoris are useful expression hosts for FIX (see for example, Skoko et al. (2003) Biotechnol. Appl. Biochem. 38(Pt3):257-65). Yeast can be transformed with episomal replicating vectors or by stable chromosomal integration by homologous recombination. Typically, inducible promoters are used to regulate gene expression. Examples of such promoters include GAL1, GAL7, and GAL5 and metallothionein promoters such as CUP1. Expression vectors often include a selectable marker such as LEU2, TRP1, HIS3, and URA3 for selection and maintenance of the transformed DNA. Proteins expressed in yeast are often soluble and co-expression with chaperonins, such as Bip and protein disulfide isomerase, can improve expression levels and solubility. Additionally, proteins expressed in yeast can be directed for secretion using secretion signal peptide fusions such as the yeast mating type alpha-factor secretion signal from Saccharomyces cerevisiae and fusions with yeast cell surface proteins such as the Aga2p mating adhesion receptor or the Arxula adeninivorans glucoamylase. A protease cleavage site (such as, the Kex-2 protease) can be engineered to remove the fused sequences from the polypeptides as they exit the secretion pathway. Yeast also is capable of glycosylation at Asn-X-Ser/Thr motifs.

c. Insects and Insect Cells

Insects and insect cells, particularly using a baculovirus expression system, are useful for expressing polypeptide such as FIX (see, for example, Muneta et al. (2003) J. Vet. Med. Sci. 65(2):219-23). Insect cells and insect larvae, including expression in the haemolymph, express high levels of protein and are capable of most of the post-translational modifications used by higher eukaryotes. Baculoviruses have a restrictive host range which improves the safety and reduces regulatory concerns of eukaryotic expression. Typically, expression vectors use a promoter such as the polyhedrin promoter of baculovirus for high level expression. Commonly used baculovirus systems include baculoviruses such as Autographa californica nuclear polyhedrosis virus (AcNPV), and the bombyx mori nuclear polyhedrosis virus (BmNPV) and an insect cell line such as Sf9 derived from Spodoptera frugiperda, Pseudaletia unipuncta (A7S) and Danaus plexippus (DpN1). For high level expression, the nucleotide sequence of the molecule to be expressed is fused immediately downstream of the polyhedrin initiation codon of the virus. Mammalian secretion signals are accurately processed in insect cells and can be used to secrete the expressed protein into the culture medium. In addition, the cell lines Pseudaletia unipuncta (A7S) and Danaus plexippus (DpN1) produce proteins with glycosylation patterns similar to mammalian cell systems.

An alternative expression system in insect cells is the use of stably transformed cells. Cell lines such as the Schnieder 2 (S2) and Kc cells (Drosophila melanogaster) and C7 cells (Aedes albopictus) can be used for expression. The Drosophila metallothionein promoter can be used to induce high levels of expression in the presence of heavy metal induction with cadmium or copper. Expression vectors are typically maintained by the use of selectable markers such as neomycin and hygromycin.

d. Mammalian Cells

Mammalian expression systems can be used to express FIX polypeptides. Expression constructs can be transferred to mammalian cells by viral infection such as adenovirus or by direct DNA transfer such as liposomes, calcium phosphate, DEAE-dextran and by physical means such as electroporation and microinjection. Expression vectors for mammalian cells typically include an mRNA cap site, a TATA box, a translational initiation sequence (Kozak consensus sequence) and polyadenylation elements. Such vectors often include transcriptional promoter-enhancers for high level expression, for example the SV40 promoter-enhancer, the human cytomegalovirus (CMV) promoter, and the long terminal repeat of Rous sarcoma virus (RSV). These promoter-enhancers are active in many cell types. Tissue and cell-type promoters and enhancer regions also can be used for expression. Exemplary promoter/enhancer regions include, but are not limited to, those from genes such as elastase I, insulin, immunoglobulin, mouse mammary tumor virus, albumin, alpha-fetoprotein, alpha 1-antitrypsin, beta-globin, myelin basic protein, myosin light chain-2, and gonadotropic releasing hormone gene control. Selectable markers can be used to select for and maintain cells with the expression construct. Examples of selectable marker genes include, but are not limited to, hygromycin B phosphotransferase, adenosine deaminase, xanthine-guanine phosphoribosyl transferase, aminoglycoside phosphotransferase, dihydrofolate reductase and thymidine kinase. Fusion with cell surface signaling molecules such as TCR-ζ and Fc_(ε)RI-γ can direct expression of the proteins in an active state on the cell surface.

Many cell lines are available for mammalian expression including mouse, rat human, monkey, chicken and hamster cells. Exemplary cell lines include, but are not limited to, CHO, Balb/3T3, HeLa, MT2, mouse NS0 (non-secreting) and other myeloma cell lines, hybridoma and heterohybridoma cell lines, lymphocytes, fibroblasts, Sp2/0, COS, NIH3T3, HEK293, 293S, 2B8, and HKB cells. Cell lines also are available adapted to serum-free media which facilitates purification of secreted proteins from the cell culture media. One such example is the serum free EBNA-1 cell line (Pham et al., (2003) Biotechnol. Bioeng. 84:332-42). Expression of recombinant wild-type FIX polypeptides exhibiting similar structure and post-translational modifications as plasma-derived FIX are known in the art (see, such as, Bon et al. (1998) Semin Hematol. 35 (2 Suppl 2): 11-17). Methods of optimizing Factor IX expression are known. For example, supplementation of vitamin K in culture medium or co-expression of vitamin K-dependent γ-carboxylases (Wajih et al., J. Biol. Chem. 280(36)31603-31607) can aid in post-translational modification of FIX polypeptides. Multiple purification steps also can aid in enriched subpopulations of FIX polypeptides with desired post-translational modifications including, γ-carboxylation, β-hydroxylation, and glycosylation.

e. Plants

Transgenic plant cells and plants can be used for the expression of FIX. Expression constructs are typically transferred to plants using direct DNA transfer such as microprojectile bombardment and PEG-mediated transfer into protoplasts, and with agrobacterium-mediated transformation. Expression vectors can include promoter and enhancer sequences, transcriptional termination elements, and translational control elements. Expression vectors and transformation techniques are usually divided between dicot hosts, such as Arabidopsis and tobacco, and monocot hosts, such as corn and rice. Examples of plant promoters used for expression include the cauliflower mosaic virus promoter, the nopaline synthase promoter, the ribose bisphosphate carboxylase promoter and the ubiquitin and UBQ3 promoters. Selectable markers such as hygromycin, phosphomannose isomerase and neomycin phosphotransferase are often used to facilitate selection and maintenance of transformed cells. Transformed plant cells can be maintained in culture as cells, aggregates (callus tissue) or regenerated into whole plants. Transgenic plant cells also can include algae engineered to produce proteins (see, for example, Mayfield et al. (2003) PNAS 100:438-442). Because plants have different glycosylation patterns than mammalian cells, this can influence the choice to produce FIX in these hosts.

2. Purification

Methods for purification of FIX polypeptides from host cells depend on the chosen host cells and expression systems. For secreted molecules, proteins are generally purified from the culture media after removing the cells. For intracellular expression, cells can be lysed and the proteins purified from the extract. When transgenic organisms such as transgenic plants and animals are used for expression, tissues or organs can be used as starting material to make a lysed cell extract. Additionally, transgenic animal production can include the production of polypeptides in milk or eggs, which can be collected, and if necessary the proteins can be extracted and further purified using standard methods in the art.

FIX can be purified using standard protein purification techniques known in the art including but not limited to, SDS-PAGE, size fraction and size exclusion chromatography, ammonium sulfate precipitation, chelate chromatography and ionic exchange chromatography. Multiple chromatographic steps can be employed to improve selection of FIX polypeptides with particular posttranslational modifications. For example, multiple chromatographic steps can be used to separate γ-carboxylated FIX polypeptides (see such as, Cott et al. (2004) Papers in Biotechnology 1-21). Such techniques also can be used to enrich for FIX polypeptides with or without modifications at particular sites, including modifications such as, but not limited to, γ-carboxylation of particular glutamic acid residues in the gla domain, phosphorylation (e.g., at S158), sulfation (such as, at Y155), and glycosylation (see such as, Kaufman et al. (1986) J Biol Chem 261: 9622-8; Harrison et al. (1998) Semin Hematol 35 (Suppl. 2): 4-10; Bond et al. (1998) Semin Hematol 35 (Suppl. 2): 11-7).

Affinity purification techniques also can be used to improve the efficiency and purity of the preparations. For example, antibodies, receptors and other molecules that bind FIX can be used in affinity purification. Expression constructs also can be engineered to add an affinity tag such as a myc epitope, GST fusion or His₆ and affinity purified with myc antibody, glutathione resin, and Ni-resin, respectively, to a protein. Purity can be assessed by any method known in the art including gel electrophoresis and staining and spectrophotometric techniques.

3. Fusion Proteins

Fusion proteins containing a targeting agent and a modified FIX polypeptide also are provided. Pharmaceutical compositions containing such fusion proteins formulated for administration by a suitable route are provided. Fusion proteins are formed by linking in any order the modified FIX polypeptide and an agent, such as an antibody or fragment thereof, growth factor, receptor, ligand, and other such agent for directing the mutant protein to a targeted cell or tissue. Linkage can be effected directly or indirectly via a linker. The fusion proteins can be produced recombinantly or chemically by chemical linkage, such as via heterobifunctional agents or thiol linkages or other such linkages. The fusion proteins can contain additional components, such as E. coli maltose binding protein (MBP) that aid in uptake of the protein by cells (see, International PCT application No. WO 01/32711). In another embodiment the modified FIX is fused to polypeptides that aid in stability, such as albumin (Sheffield et al. (2004) Br. J. Haemotol. 126(4): 565-573).

4. Polypeptide Modification

Modified FIX polypeptides can be prepared as naked polypeptide chains or as a complex. For some applications, it can be desirable to prepare modified FIX in a “naked” form without post-translational or other chemical modifications. Naked polypeptide chains can be prepared in suitable hosts that do not post-translationally modify FIX. Such polypeptides also can be prepared in in vitro systems and using chemical polypeptide synthesis. For other applications, particular modifications can be desired including pegylation, albumination, glycosylation, carboxylation, hydroxylation, phosphorylation, or other known modifications. Modifications can be made in vitro or, for example, by producing the modified FIX in a suitable host that produces such modifications.

5. Nucleotide Sequences

Nucleic acid molecules encoding modified FIX polypeptides or the fusion protein operationally linked to a promoter, such as an inducible promoter for expression in mammalian cells also are provided. Such promoters include, but are not limited to, CMV and SV40 promoters; adenovirus promoters, such as the E2 gene promoter, which is responsive to the HPV E7 oncoprotein; a PV promoter, such as the PBV p89 promoter that is responsive to the PV E2 protein; and other promoters that are activated by the HIV or PV or oncogenes.

Modified FIX polypeptides provided herein also can be delivered to cells in gene transfer vectors. The transfer vectors can encode additional therapeutic agent(s) for treatment of diseases or disorders, such as treatments for hemophilia, inherited disorders and others for which FIX is administered. Transfer vectors encoding modified FIX polypeptides can be used systemically by administering the nucleic acid to a subject. For example, the transfer vector can be a viral vector, such as an adenoviral vector. Vectors encoding FIX also can be incorporated into stem cells and such stem cells administered to a subject, for example, by transplanting or engrafting the stem cells at sites for therapy. For example, mesenchymal stem cells (MSCs) can be engineered to express a modified FIX and such MSCs engrafted at a tumor site for therapy.

G. ASSESSING MODIFIED FIX POLYPEPTIDE PROPERTIES AND ACTIVITIES

FIX activities and properties can be assessed in vitro and/or in vivo. Assays for such assessment are known to those of skill in the art and are known to correlate tested activities and results to therapeutic and in vivo activities. In one example, FIX variants can be assessed in comparison to unmodified and/or wild-type FIX. In other examples, a modified FIX polypeptide can be assessed for biological activity following in vitro or in vivo exposure to protein stability-altering conditions (i.e. exposure to proteases, or denaturing agents such as temperature or pH). In vitro assays include any laboratory assay known to one of skill in the art, such as for example, cell-based assays including coagulation assays, protein assays, and molecular biology assays. In vivo assays include FIX assays in animal models as well as administration to humans. In some cases, activity of FIX in vivo can be determined by assessing blood, serum, or other bodily fluid for assay determinants. FIX variants also can be tested in vivo to assess an activity or property, such as stability (such as, half-life) and therapeutic effect.

1. In Vitro Assays

Exemplary in vitro assays include assays to assess polypeptide stability and activity. Stability assays include assays that assess protease resistance or thermal stability or other physical property indicative of stability of the polypeptide in vivo or in vitro. Stability also can be assessed by protein structure and conformational assays known in the art. Assays for activity include, but are not limited to, measurement of FIX interaction with other coagulation cofactors, such as factor VIII, enzymatic assays to determine proteolytic activity of FIX polypeptides, and cell-based assays to determine the effect of FIX polypeptides variants on coagulation.

Concentrations of modified FIX polypeptides can be assessed by methods well-known in the art, including but not limited to enzyme-linked immunosorbant assays (ELISA), SDS-PAGE; Bradford, Lowry, BCA methods; UV absorbance, and other quantifiable protein labeling methods, such as, but not limited to, immunological, radioactive and fluorescent methods and related methods.

Assessment of cleavage products of proteolysis reactions, including cleavage of FIX polypeptides or products produced by FIX protease activity, can be performed using methods including but not limited to, chromogenic substrate cleavage, HPLC, SDS-PAGE analysis, immunohistochemistry, immunoprecipitation, NH₂-terminal sequencing, and protein labeling.

FIX polypeptides that have been activated via proteolytic cleavage after R145 and R180 can be prepared in vitro. The FIX polypeptides can be first prepared by any of the methods of production described herein, including, but not limited to, production in mammalian cells followed by purification. Cleavage of the FIX polypeptides into the active protease form of FIX can be accomplished by incubation with activated factor XI (FXIa). The activated polypeptides can be used in any of the assays to measure FIX activities described herein.

Modified FIX polypeptides can be tested for proteolytic activity. Activated forms of the modified FIX polypeptides (FIXa) can be used in the assay. Assays using a synthetic substrate, such as a CH₃SO₂-LGR-pNA peptide, can be employed to measure enzymatic cleavage activity of the FIXa polypeptides. Hydrolysis of CH₃SO₂-LGR-pNA in the presence of FIXa can be measured by assessing the production of p-nitroanaline (pNA) from the cleavage reaction sample. The amount of pNA in the sample is proportional to the absorbance of the sample at 405 nm and thus indicates the extent of proteolytic activity in the FIXa sample. Additional exemplary fluorogenic substrates that can be used to assess FIXa cleavage activity include, but are not limited to, Mes-D-CHD-Gly-Arg-AMC (Pefafluor FIXa10148) and H-D-Leu-PHG-Arg-AMC (Pefafluor FIXa3688), wherein cleavage is assessed by release of AMC. Molecules that enhance FIXa catalytic activity, such as ethylene glycol, can be employed in such assays (Sturzebecher et al. (1997) FEBS Lett. (412) 295-300).

Proteolytic activity of FIXa also can be assessed by measuring the conversion of factor X (FX) into activated factor X (FXa). Modified FIXa polypeptides can be incubated in the presence of FX polypeptides in the presence of phospholipids vesicles (phosphatidylserine and/or phosphatidylcholine) and Ca²⁺, and cleavage of FX to produce FXa can be assayed using a chromogenic substrate, such as S2222 or S2765, which is specifically cleaved by FXa (Chromogenics AB, Molndal, Sweden).

Inhibition assays can be used to measure resistance of modified FIX polypeptides to FIX inhibitors. Exemplary inhibitors include, but are not limited to, antithrombin, p-aminobenzamidine, serine protease inhibitors, and FIX-specific antibodies. Inhibitors such as antithrombin which bind to the active site of FIXa can be used in inhibition assays, such as competition assays, wherein the ability of the inhibitor to compete with another substrate is measured.

FIX polypeptides can be tested for binding to other coagulation factors and inhibitors. For example, FIX direct and indirect interactions with proteins of the tenase complex, including factors VIIIa, IXa and X, and inhibitors, such as antithrombin III and heparin can be assessed using any binding assay known in the art, including, but not limited to, immunoprecipitation, column purification, non-reducing SDS-PAGE, surface plasmon resonance (SPR), fluorescence resonance energy transfer (FRET), fluorescence polarization (FP), isothermal titration calorimetry (ITC), circular dichroism (CD), protein fragment complementation assays (PCA), Nuclear Magnetic Resonance (NMR) spectroscopy, light scattering, sedimentation equilibrium, small-zone gel filtration chromatography, gel retardation, Far-western blotting, fluorescence polarization, hydroxyl-radical protein footprinting, phage display, and various two-hybrid systems.

FIX polypeptides can be tested for coagulation activity by using assays well known in the art. For example, some of the assays include, but are not limited to, a two stage clotting assay, (Leibman, H. A. et al. (1985) Proc. Natl. Acad. Sci., USA, 82, 3879-3883); an assay based on the single stage activated partial thromboplastin time (“aPTT”), Smith, K. J. et al. (1988) Blood, 72, 1269-1277; and assays which are modifications of the aPTT test, for example, Jenny, R. et al. (1986) Preparative Biochemistry, 16, 227-245, whole blood partial thromboplastin time (PTT), activated clotting time (ACT), recalcified activated clotting time, or the Lee-White Clotting time. For the aPTT assay, coagulation activity of a FIX polypeptide can be assessed by using equal volumes of activated partial thromboplastin reagent, FIX-deficient plasma (obtained from either a patient with hemophilia B using sterile phlebotomy techniques well known in the art or by using FIX immunodepleted plasma), and normal pooled plasma as standard, or the sample. In this assay, one unit of activity is defined as that amount present in one milliliter of normal pooled plasma. Further, an assay for biological activity based on the ability of FIX to reduce the clotting time of plasma from FIX-deficient patients to normal can be performed as described in, for example, Proctor and Rapaport (1961) Amer. J. Clin. Path. 36: 212.

FIX polypeptides also can be assessed for presence of post-translational modifications. Such assays are known in the art and include assays to measure glycosylation, hydroxylation, sulfation, carboxylation, and phosphorylation. In an exemplary assay for glycosylation, carbohydrate analysis can be performed, for example, with SDS page analysis of FIX polypeptides exposed to hydrazinolysis or endoglycosidase treatment. Hydrazinolysis releases N- and O-linked glycans from glycoproteins by incubation with anhydrous hydrazine, while endoglycosidase release involves PNGase F, which releases most N-glycans from glycoproteins. Hydrazinolysis or endoglycosidase treatment of FIX polypeptides generates a reducing terminus that can be tagged with a fluorophore or chromophore label. Labeled FIX polypeptides can be analyzed by fluorophore-assisted carbohydrate electrophoresis (FACE). The fluorescent tag for glycans also can be used for monosaccharide analysis, profiling or fingerprinting of complex glycosylation patterns by HPLC. Exemplary HPLC methods include hydrophilic interaction chromatography, electronic interaction, ion-exchange, hydrophobic interaction, and size-exclusion chromatography. Exemplary glycan probes include, but are not limited to, 3-(acetylamino)-6-aminoacridine (AA-Ac) and 2-aminobenzoic acid (2-AA). Carbohydrate moieties also can be detected through use of specific antibodies that recognize the glycosylated FIX polypeptide.

An exemplary assay to measure carboxylation comprises reverse phase HPLC analysis of FIX polypeptides that have been subjected to alkaline hydrolysis (Przysiecki et al. (1987) PNAS 84: 7856-7860). Exemplary assays to measure phosphorylation include use of phosphospecific antibodies to phospho-serine and/or -tyrosine amino acid residues or to a serine-phosphorylated FIX polypeptide. ³²P metabolic labeling of cells that produce the FIX polypeptide also can be used to assess phosphorylation, wherein the labeled FIX polypeptide can be purified and analyzed for incorporation of radioactive phosphate. An exemplary assay for tyrosine sulfation includes ³⁵S labeling of cells that produce the FIX polypeptide. In such method, cells are incubated with either ³⁵S—S₂SO₄ or ³⁵S-methionine and incorporation of the ³⁵S is determined by normalization to the ³⁵S-methionine sample.

Structural properties of modified FIX polypeptides also can be assessed. For example, X-ray crystallography, nuclear magnetic resonance (NMR), and cryoelectron microscopy (cryo-EM) of modified FIX polypeptides can be performed to assess three-dimensional structure of the FIX polypeptides and/or other properties of FIX polypeptides, such as Ca²⁺or cofactor binding.

Additionally, the presence and extent of FIX degradation can be measured by standard techniques such as sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), and Western blotting of electrophoresed FIX-containing samples. FIX polypeptides that have been exposed to proteases also can be subjected to N-terminal sequencing to determine location or changes in cleavage sites if the modified FIX polypeptides.

2. Non-Human Animal Models

Non-human animal models can be used to assess activity and stability of modified FIX polypeptides. For example, non-human animals can be used as models for a disease or condition. Non-human animals can be injected with disease and/or phenotype-inducing substances prior to administration of FIX variants to monitor the effects on disease progression. Genetic models also are useful. Animals, such as mice, can be generated which mimic a disease or condition by the overexpression, underexpression or knock-out of one or more genes. Such animals can be generated by transgenic animal production techniques well-known in the art or using naturally-occurring or induced mutant strains. Examples of useful non-human animal models of diseases associated with FIX include, but are not limited to, models of bleeding disorders, in particular hemophilia, or thrombotic disease. These non-human animal models can be used to monitor activity of FIX variants compared to a wild type FIX polypeptide.

Animal models also can be used to monitor stability, half-life, and clearance of modified FIX polypeptides. Such assays are useful for comparing modified FIX polypeptides and for calculating doses and dose regimens for further non-human animal and human trials. For example, a modified FIX polypeptide can be injected into the tail vein of mice. Blood samples are then taken at time-points after injection (such as minutes, hours and days afterwards) and then the level of the modified FIX polypeptides in bodily samples including, but not limited to, serum or plasma can be monitored at specific time-points for example by ELISA or radioimmunoassay. Blood samples also can be tested for coagulation activity in methods, such as the aPTT assay.

Modified FIX polypeptides can be tested for immune tolerance using animal models. Animal models for immune tolerance of FIX are known in the art and include rhesus macaque, mouse, rat, and dog models to test long term expression of FIX via injection of polypeptides or gene transfer vectors (Lozier et al. (1999) Blood 93(6) 1875-1881 and Keith et al., (1995) Thromb. Haemost. 73(1): 101-105).

Modified FIX polypeptides can be tested for therapeutic effectiveness using animal models for hemophilia. In one non-limiting example, an animal model such as a mouse can be used. Mouse models of hemophilia are available in the art and include FIX deficient mice and mice expressing mutant FIX polypeptides, and can be employed to test modified FIX polypeptides (Wang et al. (1997) PNAS 94:11563-11566, Lin et al. (1997) Blood 90:3962-3966, Kundu et al. (1998) Blood 92: 168-174, Sabatino et al. (2004) Blood 104(9): 2767-2774 and Jin et al. (2004) Blood 104:1733-1739)

Other models of FIX deficiencies include hemophilic dogs that express defective FIX or that have been hepatectomized (Evans et al. (1989) PNAS 86:10095, Mauser et al. (1996) Blood 88:3451, and Kay et al. (1994) PNAS 91:2353-2357).

Modified FIX polypeptides can be tested for therapeutic effectiveness using animal models for thrombotic disease (Dodds (1987) Ann N Y Acad. Sci. 516: 631-635). Modified FIX polypeptides that have antithrombotic activity can be tested in such models. In one non-limiting example, an animal model such as a rat or mouse model of ischemic stroke can be used to test the effectiveness of modified FIX polypeptides. Such animal models are known in the art (Beech, et al. (2001) Brain Res 895: 18-24, Buchan et al. Stroke 23: 273-9 (1992), Carmichael et al. (2005) NeuroRx 2: 396-409, Chen et al. (1986) Stroke 17: 738-43, Gerriets et al. (2003) J Neurosci Methods 122: 201-11, Koizumi et al. (1986) Jpn. J. Stroke 8: 1-8, Longa et al. (1989) Stroke 20: 84-91, Mayzel-Oreg et al. (2004) Magn Reson Med 51: 1232-8, Tamura, et al. (1981) J Cereb Blood Flow Metab 1: 53-60, Watson et al. (1985) Ann Neurol 17: 497-504, Zhang et al. (1997) J Cereb Blood Flow Metab 17: 123-35).

3. Clinical Assays

Many assays are available to assess activity of FIX for clinical use. Such assays can include assessment of coagulation, protein stability, and half-life in vivo and phenotypic assays. Phenotypic assays and assays to assess the therapeutic effect of FIX treatment include assessment of blood levels of FIX (such as measurement of serum FIX prior to administration and time-points following administrations including, after the first administration, immediately after last administration, and time-points in between, correcting for the body mass index (BMI)), phenotypic response to FIX treatment including amelioration of symptoms over time compared to subjects treated with an unmodified and/or wild type FIX or placebo. Examples of clinical assays to assess FIX activity can be found such as in Franchini et al. (2005) Thromb Haemost. 93(6): 1027-1035, Shapiro et al. (2005) Blood 105(2): 518-525, and White et al. (1997) Thromb Haemost. 78(1): 261-265. Patients can be monitored regularly over a period of time for routine or repeated administrations, following administration in response to acute events, such as hemorrhage, trauma, or surgical procedures.

H. FORMULATION/PACKAGING/ADMINISTRATION

Pharmaceutical compositions containing an optimized polypeptide produced using methods described herein, including FIX variant (modified) polypeptides, modified FIX fusion proteins or encoding nucleic acid molecules, can be formulated in any conventional manner by mixing a selected amount of the polypeptide with one or more physiologically acceptable carriers or excipients. Selection of the carrier or excipient is within the skill of the administering profession and can depend upon a number of parameters. These include, for example, the mode of administration (i.e., systemic, oral, nasal, pulmonary, local, topical or any other mode) and disorder treated. The pharmaceutical compositions provided herein can be formulated for single dosage (direct) administration or for dilution or other modification. The concentrations of the compounds in the formulations are effective for delivery of an amount, upon administration, that is effective for the intended treatment. Typically, the compositions are formulated for single dosage administration. To formulate a composition, the weight fraction of a compound or mixture thereof is dissolved, suspended, dispersed or otherwise mixed in a selected vehicle at an effective concentration such that the treated condition is relieved or ameliorated. Pharmaceutical carriers or vehicles suitable for administration of the compounds provided herein include any such carriers known to those skilled in the art to be suitable for the particular mode of administration.

1. Administration of Modified FIX Polypeptides

The polypeptides can be formulated as the sole pharmaceutically active ingredient in the composition or can be combined with other active ingredients. The polypeptides can be targeted for delivery, such as by conjugation to a targeting agent, such as an antibody. Liposomal suspensions, including tissue-targeted liposomes, also can be suitable as pharmaceutically acceptable carriers. These can be prepared according to methods known to those skilled in the art. For example, liposome formulations can be prepared as described in U.S. Pat. No. 4,522,811. Liposomal delivery also can include slow release formulations, including pharmaceutical matrices such as collagen gels and liposomes modified with fibronectin (see, for example, Weiner et al. (1985) J Pharm Sci. 74(9): 922-5).

The active compound is included in the pharmaceutically acceptable carrier in an amount sufficient to exert a therapeutically useful effect in the absence of undesirable side effects on the subject treated. The therapeutically effective concentration can be determined empirically by testing the compounds in known in vitro and in vivo systems, such as the assays provided herein. The active compounds can be administered by any appropriate route, for example, oral, nasal, pulmonary, parenteral, intravenous, intradermal, subcutaneous, or topical, in liquid, semi-liquid or solid form and are formulated in a manner suitable for each route of administration. In a particular embodiment, the FIX polypeptide is administered orally. FIX polypeptides can be formulated with additional coagulation factors.

The modified FIX and physiologically acceptable salts and solvates can be formulated for administration by inhalation (either through the mouth or the nose), oral, transdermal, pulmonary, parenteral, or rectal administration or injection. For administration by inhalation, the modified FIX can be delivered in the form of an aerosol spray presentation from pressurized packs or a nebulizer with the use of a suitable propellant, such as, dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas. In the case of a pressurized aerosol, the dosage unit can be determined by providing a valve to deliver a metered amount. Capsules and cartridges of such as, gelatin for use in an inhaler or insufflator can be formulated containing a powder mix of a therapeutic compound and a suitable powder base such as lactose or starch.

FIX polypeptides can be formulated as liquid or powder. In the case of a liquid, the modified polypeptides can be injected from a syringe or an auto-injector. In the case of a powder, the modified polypeptides can be reconstituted with a pharmaceutically acceptable excipient, such as pharmaceutically-acceptable saline, prior to administration. Administration can be by a medical professional or self-administration.

For pulmonary administration to the lungs, the modified FIX can be delivered in the form of an aerosol spray presentation from a nebulizer, turbonebulizer, or microprocessor-controlled metered dose oral inhaler with the use of a suitable propellant. Generally, the particle size is small, such as in the range of 0.5 to 5 microns. In the case of a pharmaceutical composition formulated for pulmonary administration, detergent surfactants are not typically used. Pulmonary drug delivery is a promising non-invasive method of systemic administration. The lungs represent an attractive route for drug delivery, mainly due to the high surface area for absorption, thin alveolar epithelium, extensive vascularization, lack of hepatic first-pass metabolism, and relatively low metabolic activity.

The modified FIX polypeptides exhibit increased resistance to proteolysis and half-life in the gastrointestinal tract. Thus, preparations for oral administration can be suitably formulated without the use of protease inhibitors, such as a Bowman-Birk inhibitor, a conjugated Bowman-Birk inhibitor, aprotinin and camostat.

The modified FIX polypeptides can be formulated as a depot preparation. Such long-acting formulations can be administered by implantation (for example, subcutaneously or intramuscularly) or by intramuscular injection. Thus, for example, the therapeutic compounds can be formulated with suitable polymeric or hydrophobic materials (for example as an emulsion in an acceptable oil) or ion exchange resins, or as sparingly soluble derivatives, for example, as a sparingly soluble salt.

The modified FIX can be formulated, for example, for parenteral administration by injection (such as, by bolus injection or continuous infusion). Formulations for injection can be presented in unit dosage form (such as, in ampoules or in multi-dose containers) with an added preservative. The compositions can take such forms as suspensions, solutions or emulsions in oily or aqueous vehicles and can contain formulatory agents such as suspending, stabilizing and/or dispersing agents. Alternatively, the active ingredient can be in powder-lyophilized form for constitution with a suitable vehicle, such as, sterile pyrogen-free water, before use.

Preparations for oral administration can be suitably formulated to give controlled release of the active compound. For buccal administration the compositions can take the form of tablets or lozenges formulated in a conventional manner.

The pharmaceutical compositions can be formulated for local or topical application, such as for topical application to the skin (transdermal) and mucous membranes, such as in the eye, in the form of gels, creams, and lotions and for application to the eye or for intracisternal or intraspinal application. Such solutions, particularly those intended for ophthalmic use, can be formulated as 0.01%-10% isotonic solutions and pH about 5-7 with appropriate salts. The compounds can be formulated as aerosols for topical application, such as by inhalation (see, for example, U.S. Pat. Nos. 4,044,126, 4,414,209 and 4,364,923, which describe aerosols for delivery of a steroid useful for treatment inflammatory diseases, particularly asthma).

The concentration of active compound in the drug composition depends on absorption, inactivation and excretion rates of the active compound, the dosage schedule, and amount administered as well as other factors known to those of skill in the art. As described further herein, dosages can be determined empirically using dosages known in the art for administration of unmodified FIX, and comparisons of properties and activities (such as, stability and activities) of the modified FIX compared to the unmodified and/or native FIX.

The compositions, if desired, can be presented in a package, in a kit or dispenser device, that can contain one or more unit dosage forms containing the active ingredient. The package, for example, contains metal or plastic foil, such as a blister pack. The pack or dispenser device can be accompanied by instructions for administration. The compositions containing the active agents can be packaged as articles of manufacture containing packaging material, an agent provided herein, and a label that indicates the disorder for which the agent is provided.

a. Oral Administration

Among the modified FIX polypeptides provided herein are FIX polypeptides modified to increase protein stability to conditions amendable to oral delivery. Oral delivery can include administration to the mouth and/or gastrointestinal tract. Such modifications can include increased protein-half life under one or more conditions such as exposure to saliva, exposure to proteases in the gastrointestinal tract, exposure to increased temperature, and exposure to particular pH conditions, such as the low pH of the stomach and/or pH conditions in the intestine. For example, modifications can include resistance to one or more proteases including pepsin, trypsin, chymotrypsin, elastase, aminopeptidase, gelatinase B, gelatinase A, α-chymotrypsin, carboxypeptidase, endoproteinase Arg-C, endoproteinase Asp-N, endoproteinase Glu-C, endoproteinase Lys-C, luminal pepsin, microvillar endopeptidase, dipeptidyl peptidase, enteropeptidase, hydrolase, NS3, elastase, factor Xa, Granzyme B, thrombin, plasmin, urokinase, tPA and PSA. Modifications also can include increasing overall stability to potentially denaturing or conformation-altering conditions such as thermal tolerance, and tolerance to mixing and aeration (such as, chewing).

FIX polypeptides modified for suitability to oral delivery can be prepared using any of the methods described herein. For example, 2D- and 3D-scanning mutagenesis methods for protein rational evolution (see, co-pending U.S. Publication No. US 2005-0202438 A1 and U.S. Publication No. US-2004-0132977-A1 and published International applications WO 2004/022593 and WO 2004/022747) can be used to prepare modified FIX. Modification of FIX polypeptides for suitability for oral delivery can include removal of proteolytic digestion sites and/or increasing the overall stability of the protein structure. Such FIX variants exhibit increased protein half-life compared to an unmodified and/or wild-type native FIX in one or more conditions for oral delivery. For example, a modified FIX can have increased protein half-life and/or bioavailability in the mouth, throat (such as, through the mucosal lining), the gastrointestinal tract or systemically.

In one embodiment, the half-life of the modified FIX polypeptides provided herein is increased by an amount at least about or 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, at least 150%, at least 200%, at least 250%, at least 300%, at least 350%, at least 400%, at least 450%, at least 500% or more, when compared to the half-life of a native FIX polypeptide exposed to one or more conditions (i.e. proteases, pH, temperature) for oral delivery. In other embodiments, the half-life in vitro or in vivo (protein stability) of the modified FIX polypeptides provided herein is increased by an amount of at least 6 times, 7 times, 8 times, 9 times, 10 times, 20 times, 30 times, 40 times, 50 times, 60 times, 70 times, 80 times, 90 times, 100 times, 200 times, 300 times, 400 times, 500 times, 600 times, 700 times, 800 times, 900 times, 1000 times, or more, compared to the half-life of native FIX exposed to one or more conditions for oral delivery (i.e. proteases, pH, temperature).

In one example, half-life of the modified FIX polypeptide is assessed by increased half-life in the presence of one or more proteases. Proteases include, but are not limited to, proteases in blood, serum, the gastrointestinal tract, and the stomach. For example, proteases include, but are not limited to, pepsin, trypsin, chymotrypsin, elastase, aminopeptidase, gelatinase B, gelatinase A, α-chymotrypsin, carboxypeptidase, endoproteinase Arg-C, endoproteinase Asp-N, endoproteinase Glu-C, endoproteinase Lys-C, trypsin, luminal pepsin, microvillar endopeptidase, dipeptidyl peptidase, enteropeptidase, hydrolase, NS3, elastase, factor Xa, Granzyme B, thrombin, plasmin, urokinase, tPA and PSA. The modified polypeptide can be mixed with one or more proteases and then assessed for activity and/or protein structure after a suitable reaction time. In one embodiment, the modified polypeptide is at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% more resistant to proteolysis.

Assessment of half-life also can include exposure to increased temperature, such as the body temperature of a subject; exposure to gastric juices and/or simulated gastric juices; exposure to particular pH conditions and/or a combination of two or more conditions. Following exposure to one or more conditions, activity and/or assessment of protein structure can be used to assess the half-life of the modified FIX in comparison to an appropriate control (i.e., an unmodified and/or wild-type FIX polypeptide).

For oral administration, the pharmaceutical compositions can take the form of, for example, tablets, pills, liquid suspensions, or capsules prepared by conventional means with pharmaceutically acceptable excipients such as binding agents (such as, pregelatinized maize starch, polyvinylpyrrolidone or hydroxypropyl methylcellulose); fillers (such as, lactose, microcrystalline cellulose or calcium hydrogen phosphate); lubricants (such as, magnesium stearate, talc or silica); disintegrants (such as, potato starch or sodium starch glycolate); or wetting agents (such as, sodium lauryl sulphate). The tablets can be coated by methods well known in the art. Liquid preparations for oral administration can take the form of, for example, solutions, syrups or suspensions, or they can be presented as a dry product for constitution with water or other suitable vehicle before use. Such liquid preparations can be prepared by conventional means with pharmaceutically-acceptable saline, pharmaceutically acceptable additives such as suspending agents (such as, sorbitol syrup, cellulose derivatives or hydrogenated edible fats); emulsifying agents (such as, lecithin or acacia); non-aqueous vehicles (such as, almond oil, oily esters, ethyl alcohol or fractionated vegetable oils); and preservatives (such as, methyl or propyl-p-hydroxybenzoates or sorbic acid). The preparations also can contain buffer salts, flavoring, coloring and sweetening agents as appropriate.

The modified FIX polypeptides can be formulated for oral administration, Oral formulations include tablets, capsules, liquids or other suitable vehicle for oral administration. In some examples, the capsules or tablets are formulated with an enteric coating to be gastro-resistant. Preparation of pharmaceutical compositions containing a modified FIX for oral delivery can include formulating modified FIX polypeptides with oral formulations known in the art and/or those described herein. The compositions as formulated do not require addition of protease inhibitors and/or other ingredients that are necessary for stabilization of unmodified (for protease resistance) and wild-type FIX polypeptides upon exposure to proteases, such as selecting pH and other conditions to minimize protease cleavage. For example, such compositions exhibit stability in the absence of compounds such as actinonin or epiactinonin and derivatives thereof; Bowman-Birk inhibitor and conjugates thereof; aprotinin and camostat. In other examples, the preparations for oral administration can include protease inhibitors.

Additionally, because modified FIX polypeptides provided herein exhibit increased protein stability, there is more flexibility in the administration of pharmaceutical compositions than their unmodified counterparts. Typically, orally ingested polypeptides are administered in the morning before eating (i.e., before digestive enzymes are activated). The modified polypeptides provided herein exhibit protease resistance to digestive enzymes and can offer the ability to administer pharmaceutical compositions containing a modified FIX polypeptide at other periods during the day and under conditions when digestive enzymes are present and active.

For oral administration, the pharmaceutical compositions can take the form of, for example, tablets or capsules prepared by conventional means with pharmaceutically acceptable excipients such as binding agents (such as, pre-gelatinized maize starch, polyvinylpyrrolidone or hydroxypropyl methylcellulose); fillers (such as, lactose, microcrystalline cellulose or calcium hydrogen phosphate); lubricants (such as, magnesium stearate, talc or silica); disintegrants (such as, potato starch or sodium starch glycolate); or wetting agents (such as, sodium lauryl sulphate). The active ingredient present in the capsule can be in, for example, liquid or lyophilized form. The tablets or capsules can be coated by methods well known in the art. Tablets and capsules can be coated, for example, with an enteric coating. Liquid preparations for oral administration can take the form of, for example, solutions, syrups or suspensions, or they can be presented as a dry product for constitution with water or other suitable vehicle before use. Such liquid preparations can be prepared by conventional means with pharmaceutically acceptable additives such as suspending agents (such as, sorbitol syrup, cellulose derivatives or hydrogenated edible fats); emulsifying agents (such as, lecithin or acacia); non aqueous vehicles (such as, almond oil, oily esters, ethyl alcohol or fractionated vegetable oils); and preservatives (such as, methyl or propyl-p hydroxybenzoates or sorbic acid). The preparations also can contain buffer salts, flavoring, coloring and/or sweetening agents as appropriate.

Preparations for oral administration can be formulated to give controlled or sustained release or for release after passage through the stomach or in the small intestine of the active compound. For oral administration the compositions can take the form of tablets, capsules, liquids, lozenges and other forms suitable for oral administration. Formulations suitable for oral administration include lozenges and other formulations that deliver the pharmaceutical composition to the mucosa of the mouth, throat and/or gastrointestinal tract. Lozenges can be formulated with suitable ingredients including excipients for example, anhydrous crystalline maltose and magnesium stearate. As noted, modified polypeptides described herein exhibit resistance to blood or intestinal proteases.

The compositions for oral administration can be formulated, for example, as gastro-resistant capsules or tablets. Such gastro-resistant capsules are modified release capsules that are intended to resist the gastric fluid and to release their active ingredient or ingredients in the intestinal fluid. They are prepared by providing hard or soft capsules with a gastro-resistant shell (enteric capsules) or by filling capsules with granules or with particles covered with a gastro-resistant coating.

The enteric coating is typically, although not necessarily, a polymeric material. Enteric coating materials can contain bioerodible, gradually hydrolyzable and/or gradually water-soluble polymers. The “coating weight,” or relative amount of coating material per capsule, generally dictates the time interval between ingestion and drug release. Any coating should be applied to a sufficient thickness such that the entire coating does not dissolve in the gastrointestinal fluids at pH below about 5, but does dissolve at pH about 5 and above. It is expected that any anionic polymer exhibiting a pH-dependent solubility profile can be used as an enteric coating to achieve delivery of the active ingredient to the lower gastrointestinal tract. The selection of the specific enteric coating material will depend on the following properties: resistance to dissolution and disintegration in the stomach; impermeability to gastric fluids and drug/carrier/enzyme while in the stomach; ability to dissolve or disintegrate rapidly at the target intestine site; physical and chemical stability during storage; non-toxicity; ease of application as a coating (substrate friendly); and economical practicality.

Suitable enteric coating materials include, but are not limited to: cellulosic polymers, such as hydroxypropyl cellulose, hydroxyethyl cellulose, hydroxypropyl methyl cellulose, methyl cellulose, ethyl cellulose, cellulose acetate, cellulose acetate phthalate, cellulose acetate trimellitate, hydroxypropylmethyl cellulose phthalate, hydroxypropylmethyl cellulose succinate and carboxymethylcellulose sodium; acrylic acid polymers and copolymers, such as formed from acrylic acid, met acrylic acid, methyl acrylate, ammonium methylacrylate, ethyl acrylate, methyl methacrylate and/or ethyl methacrylate (such as, those copolymers sold under the trade name EUDRAGIT); vinyl polymers and copolymers, such as polyvinyl pyrrolidone (PVP), polyvinyl acetate, polyvinyl acetate phthalate, vinyl acetate crotonic acid copolymer, and ethylene-vinyl acetate copolymers; and shellac (purified lac). Combinations of different coating materials also can be used to coat a single capsule. Exemplary of such gastro-resistant capsules are hard gelatin capsules (sold by Torpac or Capsugel) size 9, coated with cellulose acetate phthalate (CAP) at 12% in acetone.

The enteric coating provides for controlled release of the active agent, such that drug release can be accomplished at some generally predictable location in the lower intestinal tract below the point at which drug release would occur without the enteric coating. The enteric coating also prevents exposure of the hydrophilic therapeutic agent and carrier to the epithelial and mucosal tissue of the buccal cavity, pharynx, esophagus, and stomach, and to the enzymes associated with these tissues. The enteric coating therefore helps to protect the active agent and a patient's internal tissue from any adverse event prior to drug release at the desired site of delivery. Furthermore, the coated capsules can permit optimization of drug absorption, active agent protection, and safety. Multiple enteric coatings targeted to release the active agent at various regions in the lower gastrointestinal tract would enable even more effective and sustained improved delivery throughout the lower gastrointestinal tract.

The coating optionally can contain a plasticizer to prevent the formation of pores and cracks that would permit the penetration of the gastric fluids. Suitable plasticizers include, but are not limited to, triethyl citrate (CITROFLEX 2), triacetin (glyceryl triacetate), acetyl triethyl citrate (CITROFLEC A2), CARBOWAX 400 (polyethylene glycol 400), diethyl phthalate, tributyl citrate, acetylated monoglycerides, glycerol, fatty acid esters, propylene glycol, and dibutyl phthalate. In particular, a coating comprised of an anionic carboxylic acrylic polymer will typically contain less than about 50% by weight, such as less than about 30%, 10% to about 25% by weight, based on the total weight of the coating, of a plasticizer, particularly dibutyl phthalate, polyethylene glycol, triethyl citrate and triacetin. The coating also can contain other coating excipients, such as detackifiers, antifoaming agents, lubricants (such as, magnesium stearate), and stabilizers (such as, hydroxypropylcellulose, acids and bases) to solubilize or disperse the coating material, and to improve coating performance and the coated product.

The coating can be applied to the capsule or tablet using conventional coating methods and equipment. For example, an enteric coating can be applied to a capsule using a coating pan, an airless spray technique, fluidized bed coating equipment, or the like. Detailed information concerning materials, equipment and processes for preparing coated dosage forms are described in Pharmaceutical Dosage Forms: Tablets, eds. Lieberman et al. (New York: Marcel Dekker, Inc., 1989), and in Ansel et al., Pharmaceutical Dosage Forms and Drug Delivery Systems, 6^(th) Edition (Media, Pa.: Williams & Wilkins, 1995). The coating thickness, as noted above, must be sufficient to ensure that the oral dosage form remains intact until the desired site of topical delivery in the lower intestinal tract is reached.

Preparations for oral administration can be formulated to give controlled or sustained release or for release after passage through the stomach or in the small intestine of the active compound. For oral administration the compositions can take the form of tablets, capsules, liquids, lozenges and other forms suitable for oral administration Formulations suitable for oral administration include lozenges and other formulations that deliver the pharmaceutical composition to the mucosa of the mouth, throat and/or gastrointestinal tract. Lozenges can be formulated with suitable ingredients including excipients for example, anhydrous crystalline maltose and magnesium stearate. As noted, modified polypeptides herein exhibit resistance to blood or intestinal proteases and can exhibit increased half-life in the gastrointestinal tract. Thus, preparations of oral administration can be suitably formulated without additional protease inhibitors or other protective compounds, such as a Bowman-Birk inhibitor, a conjugated Bowman-Birk inhibitor, aprotinin and camostat. Preparations for oral administration also can include a modified FIX resistant to proteolysis formulated with one or more additional ingredients that also confer proteases resistance, or confer stability in other conditions, such as particular pH conditions.

2. Administration of Nucleic Acids Encoding Modified FIX Polypeptides (Gene Therapy)

Also provided are compositions of nucleic acid molecules encoding the modified FIX polypeptides and expression vectors encoding them that are suitable for gene therapy. Rather than deliver the protein, nucleic acid can be administered in vivo, such as systemically or by other route, or ex vivo, such as by removal of cells, including lymphocytes, introduction of the nucleic therein, and reintroduction into the host or a compatible recipient.

Modified FIX polypeptides can be delivered to cells and tissues by expression of nucleic acid molecules. Modified FIX polypeptides can be administered as nucleic acid molecules encoding modified FIX polypeptides, including ex vivo techniques and direct in vivo expression. Nucleic acids can be delivered to cells and tissues by any method known to those of skill in the art. The isolated nucleic acid sequences can be incorporated into vectors for further manipulation.

Methods for administering modified FIX polypeptides by expression of encoding nucleic acid molecules include administration of recombinant vectors. The vector can be designed to remain episomal, such as by inclusion of an origin of replication or can be designed to integrate into a chromosome in the cell. Modified FIX polypeptides also can be used in ex vivo gene expression therapy using non-viral vectors. For example, cells can be engineered to express a modified FIX polypeptide, such as by integrating a modified FIX polypeptide encoding-nucleic acid into a genomic location, either operatively linked to regulatory sequences or such that it is placed operatively linked to regulatory sequences in a genomic location. Such cells then can be administered locally or systemically to a subject, such as a patient in need of treatment.

Viral vectors, include, for example adenoviruses, adeno-associated viruses (AAV), poxviruses, herpes viruses, retroviruses and others designed for gene therapy can be employed. The vectors can remain episomal or can integrate into chromosomes of the treated subject. A modified FIX polypeptide can be expressed by a virus, which is administered to a subject in need of treatment. Viral vectors suitable for gene therapy include adenovirus, adeno-associated virus (AAV), retroviruses, lentiviruses, vaccinia viruses and others noted above. For example, adenovirus expression technology is well-known in the art and adenovirus production and administration methods also are well known. Adenovirus serotypes are available, for example, from the American Type Culture Collection (ATCC, Rockville, Md.). Adenovirus can be used ex vivo, for example, cells are isolated from a patient in need of treatment, and transduced with a modified FIX polypeptide-expressing adenovirus vector. After a suitable culturing period, the transduced cells are administered to a subject, locally and/or systemically. Alternatively, modified FIX polypeptide-expressing adenovirus particles are isolated and formulated in a pharmaceutically-acceptable carrier for delivery of a therapeutically effective amount to prevent, treat or ameliorate a disease or condition of a subject. Typically, adenovirus particles are delivered at a dose ranging from 1 particle to 1014 particles per kilogram subject weight, generally between 106 or 108 particles to 1012 particles per kilogram subject weight. In some situations it is desirable to provide a nucleic acid source with an agent that targets cells, such as an antibody specific for a cell surface membrane protein or a target cell, or a ligand for a receptor on a target cell. FIX also can be targeted for delivery into specific cell types. For example, adenoviral vectors encoding FIX polypeptides can be used for stable expression in nondividing cells, such as liver cells, and skeletal muscle cells (Arruda et al. (2001) Blood 97(1): 130-138 and Yao et al. (1992) PNAS 89: 3357-3361). In another example, viral or nonviral vectors encoding FIX polypeptides can be transduced into isolated cells for subsequent delivery. Additional cell types for expression and delivery of FIX are known in the art and include but are not limited to, fibroblasts and endothelial cells (Palmer et al. (1989) Blood 73: 438-445; Yao et al. (1991) PNAS 88: 8101-8105).

The nucleic acid molecules can be introduced into artificial chromosomes and other non-viral vectors. Artificial chromosomes, such as ACES (see, Lindenbaum et al. Nucleic Acids Res. 2004 Dec. 7; 32(21):e172) can be engineered to encode and express the isoform. Briefly, mammalian artificial chromosomes (MACs) provide a means to introduce large payloads of genetic information into the cell in an autonomously replicating, non-integrating format. Unique among MACs, the mammalian satellite DNA-based Artificial Chromosome Expression (ACE) can be reproducibly generated de novo in cell lines of different species and readily purified from the host cells' chromosomes. Purified mammalian ACEs can then be re-introduced into a variety of recipient cell lines where they have been stably maintained for extended periods in the absence of selective pressure using an ACE System. Using this approach, specific loading of one or two gene targets has been achieved in LMTK(−) and CHO cells.

Another method for introducing nucleic acids encoding the modified FIX polypeptides is a two-step gene replacement technique in yeast, starting with a complete adenovirus genome (Ad2; Ketner et al. (1994) Proc. Natl. Acad. Sci. USA 91: 6186-6190) cloned in a Yeast Artificial Chromosome (YAC) and a plasmid containing adenovirus sequences to target a specific region in the YAC clone, an expression cassette for the gene of interest and a positive and negative selectable marker. YACs are of particular interest because they permit incorporation of larger genes. This approach can be used for construction of adenovirus-based vectors bearing nucleic acids encoding any of the described modified FIX polypeptides for gene transfer to mammalian cells or whole animals.

The nucleic acids can be encapsulated in a vehicle, such as a liposome, or introduced into cells, such as a bacterial cell, particularly an attenuated bacterium or introduced into a viral vector. For example, when liposomes are employed, proteins that bind to a cell surface membrane protein associated with endocytosis can be used for targeting and/or to facilitate uptake, such as capsid proteins or fragments thereof tropic for a particular cell type, antibodies for proteins which undergo internalization in cycling, and proteins that target intracellular localization and enhance intracellular half-life.

For ex vivo and in vivo methods, nucleic acid molecules encoding the modified FIX polypeptide is introduced into cells that are from a suitable donor or the subject to be treated. Cells into which a nucleic acid can be introduced for purposes of therapy include, for example, any desired, available cell type appropriate for the disease or condition to be treated, including but not limited to epithelial cells, endothelial cells, keratinocytes, fibroblasts, muscle cells, hepatocytes; blood cells such as T lymphocytes, B lymphocytes, monocytes, macrophages, neutrophils, eosinophils, megakaryocytes, granulocytes; various stem or progenitor cells, in particular hematopoietic stem or progenitor cells, such as, such as stem cells obtained from bone marrow, umbilical cord blood, peripheral blood, fetal liver, and other sources thereof.

For ex vivo treatment, cells from a donor compatible with the subject to be treated or the subject to be treated cells are removed, the nucleic acid is introduced into these isolated cells and the modified cells are administered to the subject. Treatment includes direct administration, such as, for example, encapsulated within porous membranes, which are implanted into the patient (see, such as, U.S. Pat. Nos. 4,892,538 and 5,283,187 each of which is herein incorporated by reference in its entirety). Techniques suitable for the transfer of nucleic acid into mammalian cells in vitro include the use of liposomes and cationic lipids (such as, DOTMA, DOPE and DC-Chol) electroporation, microinjection, cell fusion, DEAE-dextran, and calcium phosphate precipitation methods. Methods of DNA delivery can be used to express modified FIX polypeptides in vivo. Such methods include liposome delivery of nucleic acids and naked DNA delivery, including local and systemic delivery such as using electroporation, ultrasound and calcium-phosphate delivery. Other techniques include microinjection, cell fusion, chromosome-mediated gene transfer, microcell-mediated gene transfer and spheroplast fusion.

In vivo expression of a modified FIX polypeptide can be linked to expression of additional molecules. For example, expression of a modified FIX polypeptide can be linked with expression of a cytotoxic product such as in an engineered virus or expressed in a cytotoxic virus. Such viruses can be targeted to a particular cell type that is a target for a therapeutic effect. The expressed modified FIX polypeptide can be used to enhance the cytotoxicity of the virus.

In vivo expression of a modified FIX polypeptide can include operatively linking a modified FIX polypeptide encoding nucleic acid molecule to specific regulatory sequences such as a cell-specific or tissue-specific promoter. Modified FIX polypeptides also can be expressed from vectors that specifically infect and/or replicate in target cell types and/or tissues. Inducible promoters can be used to selectively regulate modified FIX polypeptide expression. An exemplary regulatable expression system is the doxycycline-inducible gene expression system, which has been used to regulate recombinant FIX expression (Srour et al. Thromb Haemost. 90(3): 398-405 (2003)).

Nucleic acid molecules, as naked nucleic acids or in vectors, artificial chromosomes, liposomes and other vehicles can be administered to the subject by systemic administration, topical, local and other routes of administration. When systemic and in vivo, the nucleic acid molecule or vehicle containing the nucleic acid molecule can be targeted to a cell.

Administration also can be direct, such as by administration of a vector or cells that typically targets a cell or tissue. For example, tumor cells and proliferating cells can be targeted cells for in vivo expression of modified FIX polypeptides. Cells used for in vivo expression of a modified FIX polypeptide also include cells autologous to the patient. Such cells can be removed from a patient, nucleic acids for expression of an modified FIX polypeptide introduced, and then administered to a patient such as by injection or engraftment.

Polynucleotides and expression vectors provided herein can be made by any suitable method. Further provided are nucleic acid vectors comprising nucleic acid molecules as described above, including a nucleic acid molecule comprising a sequence of nucleotides that encodes the polypeptide as set forth in any of SEQ ID NOS: 3-891, 917-1034, 1036-2044 or a fragment thereof. Further provided are nucleic acid vectors comprising nucleic acid molecules as described above and cells containing these vectors.

I. THERAPEUTIC USES

The modified FIX polypeptides and nucleic acid molecules provided herein can be used for treatment of any condition for which unmodified FIX is employed. Modified FIX polypeptides have therapeutic activity alone or in combination with other agents. The modified polypeptides provided herein are designed to retain therapeutic activity but exhibit modified properties, particularly increased stability. Such modified properties, for example, can improve the therapeutic effectiveness of the polypeptides and/or can provide for additional routes of administration, such as oral administration. The modified FIX polypeptides and encoding nucleic acid molecules provided herein can be used for treatment of any condition for which unmodified FIX is employed. This section provides exemplary uses of and administration methods. These described therapies are exemplary and do not limit the applications of modified FIX polypeptides.

The modified FIX polypeptides provided herein can be used in various therapeutic as well as diagnostic methods in which FIX is employed. Such methods include, but are not limited to, methods of treatment of physiological and medical conditions described and listed below. Modified FIX polypeptides provided herein can exhibit improvement of in vivo activities and therapeutic effects compared to wild-type FIX, including lower dosage to achieve the same effect, a more sustained therapeutic effect and other improvements in administration and treatment.

The modified FIX polypeptides described herein exhibit increased protein stability and improved half-life. Thus, modified FIX polypeptides can be used to deliver longer-lasting, more stable therapies. Examples of therapeutic improvements using modified FIX polypeptides include, but are not limited to, lower dosages, fewer and/or less frequent administrations, decreased side effects and increased therapeutic effects.

In particular, modified FIX polypeptides, are intended for use in therapeutic methods in which FIX has been used for treatment. Such methods include, but are not limited to, methods of treatment of diseases and disorders, such as, but not limited to, blood coagulation disorders, hematologic diseases, hemorrhagic disorders, hemophilias, in particular hemophilia B, and acquired blood disorders, such as caused by liver disease. Modified FIX polypeptides also can be used in the treatment of additional bleeding diseases and disorders, such as, but not limited to, thrombocytopenia (such as, idiopathic thrombocytopenic purpura, and thrombotic thrombocytopenic purpura), Von Willebrand's disease, hereditary platelet disorders (such as, storage pool disease such as Chediak-Higashi and Hermansky-Pudlak syndromes, thromboxane A2 dysfunction, thromboasthenia, and Bernard-Soulier syndrome), hemolytic-uremic syndrome, Hereditary Hemorhhagic Telangiectsia, also known as Rendu-Osler-Weber syndrome, allergic purpura (Henoch Schonlein purpura) and disseminated intravascular coagulation. In some embodiments, the bleedings to be treated by FIX polypeptides occur in organs such as the brain, inner ear region, eyes, liver, lung, tumor tissue, gastrointestinal tract. In other embodiments, the bleeding is diffuse, such as in haemorrhagic gastritis and profuse uterine bleeding. Patients with bleeding disorders are often at risk for hemorrhage and excessive bleeding during surgery or trauma. Such patients often have acute haemarthroses (bleedings in joints), chronic haemophilic arthropathy, haematomas, (such as, muscular, retroperitoneal, sublingual and retropharyngeal), bleedings in other tissue, haematuria (bleeding from the renal tract), cerebral hemorrhage, surgery (such as, hepatectomy), dental extraction, and gastrointestinal bleedings (such as, UGI bleeds), that can be treated with modified FIX polypeptides. In one embodiment, the modified FIX polypeptides can be used to treat bleeding episodes due to trauma, or surgery, or lowered count or activity of platelets, in a subject. Exemplary methods for patients undergoing surgery include treatments to prevent hemorrhage and treatments before, during, or after surgeries such as, but not limited to, heart surgery, angioplasty, lung surgery, abdominal surgery, spinal surgery, brain surgery, vascular surgery, dental surgery, or organ transplant surgery, including transplantation of heart, lung, pancreas, or liver.

FIX polypeptides lacking functional peptidase activity have been used in therapeutic methods to inhibit blood coagulation (U.S. Pat. No. 6,315,995). Modified FIX polypeptides provided herein that inhibit or antagonize blood coagulation can be used in anticoagulant methods of treatment for ischemic disorders, such as a peripheral vascular disorder, a pulmonary embolus, a venous thrombosis, deep vein thrombosis (DVT), superficial thrombophlebitis (SVT), arterial thrombosis, a myocardial infarction, a transient ischemic attack, unstable angina, a reversible ischemic neurological deficit, an adjunct thrombolytic activity, excessive clotting conditions, reperfusion injury, sickle cell anemia or stroke disorder. In patients with an increased risk of excessive clotting, such as DVT or SVT, during surgery, protease inactive modified FIX polypeptides provided herein can be administered to prevent excessive clotting in surgeries, such as, but not limited to heart surgery, angioplasty, lung surgery, abdominal surgery, spinal surgery, brain surgery, vascular surgery, or organ transplant surgery, including transplantation of heart, lung, pancreas, or liver. In some cases treatment is performed with FIX alone. In some cases, FIX is administered in conjunction with additional coagulation or anticoagulation factors as required by the condition or disease to be treated.

Treatment of diseases and conditions with modified FIX polypeptides can be effected by any suitable route of administration using suitable formulations as described herein including, but not limited to, injection, pulmonary, oral and transdermal administration. If necessary, a particular dosage and duration and treatment protocol can be empirically determined or extrapolated. For example, exemplary doses of recombinant and native FIX polypeptides can be used as a starting point to determine appropriate dosages. For example, a recombinant FIX polypeptide, BeneFIX®, has been administered to patients with hemophilia B, at a dosage of 50 I.U./kg over a 10 minute infusion, resulting in a mean circulating activity of 0.8±0.2 I.U./dL per I.U./kg infused with a mean half-life of 19.4±5.4 hours. Modified FIX polypeptides that are more stable and have an increased half-life in vivo, can be effective at reduced dosage amounts and or frequencies. For example, because of the improvement in properties such as serum stability, dosages can be lower than comparable amounts of unmodified FIX. Dosages for unmodified FIX polypeptides can be used as guidance for determining dosages for modified FIX polypeptides. Factors such as the level of activity and half-life of the modified FIX in comparison to the unmodified FIX can be used in making such determinations. Particular dosages and regimens can be empirically determined.

Dosage levels and regimens can be determined based upon known dosages and regimens, and, if necessary can be extrapolated based upon the changes in properties of the modified polypeptides and/or can be determined empirically based on a variety of factors. Such factors include body weight of the individual, general health, age, the activity of the specific compound employed, sex, diet, time of administration, rate of excretion, drug combination, the severity and course of the disease, and the patient's disposition to the disease and the judgment of the treating physician. The active ingredient, the polypeptide, typically is combined with a pharmaceutically effective carrier. The amount of active ingredient that can be combined with the carrier materials to produce a single dosage form or multi-dosage form can vary depending upon the host treated and the particular mode of administration.

The effect of the FIX polypeptides on the clotting time of blood can be monitored using any of the clotting tests known in the art including, but not limited to, whole blood partial thromboplastin time (PTT), the activated partial thromboplastin time (aPTT), the activated clotting time (ACT), the recalcified activated clotting time, or the Lee-White Clotting time.

Upon improvement of a patient's condition, a maintenance dose of a compound or compositions can be administered, if necessary; and the dosage, the dosage form, or frequency of administration, or a combination thereof can be modified. In some cases, a subject can require intermittent treatment on a long-term basis upon any recurrence of disease symptoms or based upon scheduled dosages. In other cases, additional administrations can be required in response to acute events such as hemorrhage, trauma, or surgical procedures.

The following are some exemplary conditions for which FIX has been used as a treatment agent alone or in combination with other agents.

1. Hemophilia

Hemophilia is a bleeding disorder that is caused by a deficiency in one or more blood coagulation factors. It is characterized by a decreased ability to form blood clots at sites of tissue damage. Congenital X-linked hemophilias include hemophilia A and hemophilia B, or Christmas disease, which are caused by deficiencies in FVIII and FIX, respectively. Hemophilia A occurs at a rate of 1 out of 10,0000 males, while hemophilia B occurs in 1 out of 50,000 males.

Patients with hemophilia suffer from recurring joint and muscle bleeds, which can be spontaneous or in response to trauma. The bleeding can cause severe acute pain, restrict movement, and lead to secondary complications including synovial hypertrophy. Furthermore, the recurring bleeding in the joints can cause chronic synovitis, which can cause joint damage, destroying synovium, cartilage, and bone.

Hemophilia B can be effectively managed with administration of FIX therapeutics. Patients can often achieve normal life span with proper treatment to control bleeding episodes. Administration of FIX can aid in controlling bleeding during surgery, trauma, during dental extraction, or to alleviate bleeding associated with hemarthroses, hematuria, mucocutaneous bleeding, such as epistaxis or gastrointestinal tract bleeding, cystic lesions in subperiosteal bone or soft tissue, or hematomas, which cause neurological complications such as intracranial bleeding, spinal canal bleeding. Death in patients with hemophilia is often the result of bleeding in the central nervous system. Other serious complications in hemophilic patients include development of inhibitors to coagulation factor therapeutics and disease, such as progressive hepatitis with hepatic failure or AIDS caused by use of contaminated blood products.

The most frequent alterations in the FIX gene are point mutations, in particular missense mutations. Most of the identified FIX mutations occur in amino acid residues in the coding region of the FIX gene, often affecting evolutionarily conserved amino acids. The severity of the hemophilia depends upon the nature of the mutation. Mutations in the coding region can affect a number of different properties or activities of the FIX polypeptide including alteration of protease activity, cofactor binding, signal peptide or propeptide cleavage, post-translational modifications, and inhibition of cleavage of FIX into its activated form. Other types of point mutations include nonsense mutations that produce an unstable truncated FIX polypeptide, and frameshift mutations (small deletions and insertions) that result in a terminally aberrant FIX molecule. In addition, FIX point mutations can be found in the promoter region, which can disrupt the recognition sequences for several specific gene regulatory proteins, resulting in reduced transcription of coagulation factor IX. Decreased FIX as a result of transcriptional abnormalities is called Hemophilia B Leyden. An exemplary mutation in the promoter region includes disruption of the HNF-4 binding site, which affect regulation of FIX transcription by the androgen receptor. The severity of this type of hemophilia is governed by the levels of androgen in the blood, which increase during puberty and partially alleviate the FIX transcriptional deficiency (Kurachi et al. (1995)). Other missense nucleotide changes affect the processing of factor IX primary RNA transcript. For example, some mutations occur at evolutionarily conserved donor-splice (GT), and acceptor-splice (AG) consensus sequences, which can create cryptic splice junctions and disrupt assembly of spliceosomes. Some severe cases of hemophilia (approximately 10%) present with large deletions in the FIX gene (Gianelli et al. (1998). Treatment of FIX deficiency most often involves administration of FIX in the form of purified plasma concentrates, purified FIX preparations, or recombinant forms of FIX. Occasionally patients with large deletions produce anti-FIX antibodies, or inhibitors, in response to replacement therapy (Gianelli et al. (1983)). Among purified FIX therapeutics available for the treatment of hemophilia are: MonoNine® (Aventis Behring), Alpha-nine-SD® (Alpha therapeutic), and BeneFix® (Genetics Institute). MonoNine® and Alpha-nine-SD® are FIX preparations derived from human plasma, while BeneFix® is a recombinant FIX generated from the native FIX polypeptide sequence. FIX complex therapeutics include Bebulin® VII, a purified concentrate of FIX with FX and low amounts of FVII; Konyne® 80 (Bayer), a purified concentrate of FIX, with FII, FX, and low levels of FVII; PROPLEX® T (Baxter International), a heat treated product prepared from pooled normal human plasma containing FIX with FII, FVII, and FX; and Profilnine SD® (Alpha Therapeutic Corporation), a solvent detergent treated, concentrate of FIX with FII, FX and low levels of FVII. All such products can be modified as described herein and/or replaced with modified FIX polypeptides provided herein.

The modified FIX polypeptides provided herein and the nucleic acids encoding the modified FIX polypeptides provided herein can be used in therapies for hemophilia, including treatment of bleeding conditions associated with hemophilia. The modified FIX polypeptides provided herein can be used, for example, to control or prevent spontaneous bleeding episodes or to control or prevent bleeding in response to trauma or surgical procedures. In one embodiment, the modified FIX polypeptides herein, and nucleic acids encoding modified FIX polypeptides can be used for treatment of hemophilia B. The modified FIX polypeptides herein provide increased protein stability and increased protein half-life. Of particular interest are FIX polypeptides that are resistant to proteases. Thus, modified FIX polypeptides can be used to deliver longer lasting, more stable therapies for hemophilia. Examples of therapeutic improvements using modified FIX polypeptides include for example, but are not limited to, lower dosages, fewer and/or less frequent administrations, decreased side effects, and increased therapeutic effects. Modified FIX polypeptides can be tested for therapeutic effectiveness, for example, by using animal models. For example FIX-deficient mice, or any other known disease model for hemophilia, can be treated with modified FIX polypeptides. Progression of disease symptoms and phenotypes is monitored to assess the effects of the modified FIX polypeptides. Modified FIX polypeptides also can be administered to animal models as well as subjects such as in clinical trials to assess in vivo effectiveness in comparison to placebo controls and/or controls using unmodified FIX.

The modified FIX polypeptide can be used to deliver longer lasting, more stable hemophilia B therapies. Thus, the modified FIX polypeptides provided herein can be administered at lower dosages and/or less frequently then unmodified or native FIX polypeptides, such as MonoNine® or Alpha-nine-SD®, or recombinant forms of FIX, such as BeneFix®, while retaining one or more therapeutic activities and/or having one or more fewer/decreased side effects.

2. Thrombotic Diseases and Conditions

Thrombotic diseases are characterized by hypercoagulation, or the deregulation of hemostasis in favor of development of blot clots. Exemplary thrombotic diseases and conditions include arterial thrombosis, venous thrombosis, venous thromboembolism, pulmonary embolism, deep vein thrombosis, stroke, ischemic stroke, myocardial infarction, unstable angina, atrial fibrillation, renal damage, percutaneous translumenal coronary angioplasty, disseminated intravascular coagulation, sepsis, artificial organs, shunts or prostheses, and other acquired thrombotic diseases, as discussed below. Typical therapies for thrombotic diseases involve anticoagulant therapies, including inhibition of the coagulation cascade.

The modified FIX polypeptides provided herein and the nucleic acids encoding the modified FIX polypeptides provided herein can be used in anticoagulant therapies for thrombotic diseases and conditions, including treatment of conditions involving intravascular coagulation. The modified FIX polypeptides provided herein that can inhibit blood coagulation can be used, for example, to control or prevent formation of thromboses. In a particular embodiment, the modified FIX polypeptides herein, and nucleic acids encoding modified FIX polypeptides can be used for treatment of an arterial thrombotic disorder. In another embodiment, the modified FIX polypeptides herein, and nucleic acids encoding modified FIX polypeptides can be used for treatment of a venous thrombotic disorder, such as deep vein thrombosis. In a particular embodiment, the modified FIX polypeptides herein, and nucleic acids encoding modified FIX polypeptides can be used for treatment of an ischemic disorder, such as stroke. The modified FIX polypeptides herein provide increased protein stability and increased protein half-life. Of particular interest are FIX polypeptides that are resistant to proteases. Thus, modified FIX polypeptides can be used to deliver longer lasting, more stable therapies for thrombotic diseases and conditions. Examples of therapeutic improvements using modified FIX polypeptides include for example, but are not limited to, lower dosages, fewer and/or less frequent administrations, decreased side effects, and increased therapeutic effects. Modified FIX polypeptides can be tested for therapeutic effectiveness, for example, by using animal models. For example mouse models of ischemic stroke, or any other known disease model for a thrombotic disease or condition, can be treated with modified FIX polypeptides (Dodds (1987) Ann NY Acad Sci 516: 631-635). Progression of disease symptoms and phenotypes is monitored to assess the effects of the modified FIX polypeptides. Modified FIX polypeptides also can be administered to animal models as well as subjects such as in clinical trials to assess in vivo effectiveness in comparison to placebo controls and/or controls using unmodified FIX.

a. Arterial Thrombosis

Arterial thrombi form as a result of a rupture in the arterial vessel wall. Most often the rupture occurs in patients with vascular disease, such as atherosclerosis. The arterial thrombi usually form in regions of disturbed blood flow and at sites of rupture due to an atherosclerotic plaque, which exposes the thrombogenic subendothelium to platelets and coagulation proteins, which in turn activate the coagulation cascade. Plaque rupture may also produce further narrowing of the blood vessel due to hemorrhage into the plaque. Nonocclusive thrombi can become incorporated into the vessel wall and can accelerate the growth of atherosclerotic plaques. Formation arterial thrombi can result in ischemia either by obstructing flow or by embolism into the distal microcirculation. Anticoagulants and drugs that suppress platelet function and the coagulation cascade can be effective in the prevention and treatment of arterial thrombosis. Such classes of drugs are effective in the treatment of arterial thrombosis. Arterial thrombosis can lead to conditions of unstable angina and acute myocardial infarction. Modified FIX polypeptides provided herein that inhibit coagulation can be used in the treatment and/or prevention of arterial thrombosis and conditions, such as unstable angina and acute myocardial infarction.

b. Venous Thrombosis and Thromboembolism

Venous thrombosis is a condition in the which a blood clot forms in a vein due to imbalances in the signals for clot formation versus clot dissolution, especially in instances of low blood flow through the venous system. Results of thrombus formation can include damage to the vein and valves of the vein, though the vessel wall typically remains intact. The clots can often embolize, or break off, and travel through the blood stream where they can lodge into organ areas such as the lungs (pulmonary embolism), brain (ischemic stroke, transient ischemic attack), heart (heart attack/myocardial infarction, unstable angina), skin (purpura fulminans), and adrenal gland. In some instances the blockage of blood flow can lead to death. Patients with a tendency to have recurrent venous thromboembolism are characterized as having thrombophilia. Risk factors for developing thromboembolic disease include trauma, immobilization, malignant disease, heart failure, obesity, high levels of estrogens, leg paralysis, myocardial infarction, varicose veins, cancers, dehydration, smoking, oral contraceptives, and pregnancy. Genetic studies of families with thrombophilia have shown inheritable high levels coagulation factors, including FVIII, FIX, and FXI (Lavigne et al. (2003) J. Thromb. Haemost. 1:2134-2130).

Deep vein thrombosis (DVT) refers the formation of venous blot clot in the deep leg veins. The three main factors that contribute to DVT are injury to the vein lining, increased tendency for the blood to clot and slowing of blood flow. Collectively, these factor are called Virchow's triad. Veins can become injured during trauma or surgery, or as a result of disease condition, such as Buerger's disease or DIC, or another clot. Other contributing factors to development of DVT are similar to that of more general thromboembolic diseases as discussed above. The clot that forms in DVT causes only minor inflammation, thus, allowing it to break loose into the blood stream more easily. Often the thrombus can break off as a result of minor contraction of the leg muscles. Once the thrombus becomes an embolus it can become lodged into vessels of the lungs where is can cause a pulmonary infarction. Patients with high levels of active FIX in their bloodstream are at an increased risk of developing deep vein thrombosis (Weltermann et al. (2003) J. Thromb. Haemost. 1(1): 16-18).

Thromboembolic disease can be hereditary, wherein the disease is caused by hereditary abnormalities in clotting factors, thus leading to the imbalance in hemostasis. Several congenital deficiencies include antithrombin III, protein C, protein S, or plasminogen. Other factors include resistance to activated protein C (also termed APC resistance or Factor V leiden effect, in which a mutation in factor V makes it resistant to degradation by protein C), mutation in prothrombin, dysfibrinogemia (mutations confer resistance to fibrinolysis), and hyperhomocysteinemia. Development of thrombombolic disease in younger patients is most often due to the congenital defects described above and is called Juvenile Thrombophilia.

Treatments for venous thromboembolic disease and DVT typically involve anticoagulant therapy, in which oral doses of heparin and warfarin are administered. Heparin is usually infused into patients to control acute events, followed by longer term oral anticoagulant therapy with warfarin to control future episodes. Other therapies include direct thrombin inhibitors, inhibitors of platelet function, such as aspirin and dextran, and therapies to counteract venous stasis, including compression stockings and pneumatic compression devices. Modified FIX polypeptides provided herein that inhibit blood coagulation can be used in anticoagulant therapies for thromboembolic disease and/or DVT. In some embodiments, modified FIX polypeptides provided herein that inhibit blood coagulation can be used in prevention therapies for thromboembolic disease and/or DVT in patients exhibiting risk factors for thromboembolic disease and/or DVT. Modified FIX polypeptides provided herein that inhibit coagulation can be used in anticoagulation therapies for thromboembolic disease and/or DVT due to high levels of FIX in the blood stream.

i. Ischemic Stroke

Ischemic stroke occurs when the blood flow to the brain is interrupted, wherein the sudden loss of circulation to an area of the brain results in a corresponding loss of neurologic function. In contrast to a hemorrhagic stroke, which is characterized by intracerebral bleeding, an ischemic stroke is usually caused by thrombosis or embolism. Ischemic strokes account for approximately 80% of all strokes. In addition to the causes and risk factors for development a thromboembolism as discussed above, processes that cause dissection of the cerebral arteries (such as, trauma, thoracic aortic dissection, arteritis) can cause thrombotic stroke. Other causes include hypoperfusion distal to a stenotic or occluded artery or hypoperfusion of a vulnerable watershed region between 2 cerebral arterial territories. Treatments for ischemic stroke involve anticoagulant therapy for the prevention and treatment of the condition. Modified FIX polypeptides provided herein that inhibit coagulation can be used in the treatment and/or prevention or reduction of risk of ischemic stroke.

3. Acquired Coagulation Disorders

Acquired coagulation disorders are the result of conditions or diseases, such as vitamin K deficiency, liver disease, disseminated intravascular coagulation (DIC), or development of circulation anticoagulants. The defects in blood coagulation are the result of secondary deficiencies in clotting factors caused by the condition or disease. For example, production of coagulation factors from the liver is often impaired when the liver is in a diseased state. Along with decreased synthesis of coagulation factors, fibrinolysis becomes increased and thrombocytopenia (deficiency in platelets) is increased. Decreased production of coagulation factors by the liver also can result from fulminant hepatitis or acute fatty liver of pregnancy. Such conditions promote intravascular clotting which consumes available coagulation factors. Modified FIX polypeptides provided herein can be used in the treatment of acquired coagulation disorders in order to alleviate deficiencies in blood clotting factors.

a. Disseminated Intravascular Coagulation (DIC)

Disseminated intravascular coagulation (DIC) is a disorder characterized by a widespread and ongoing activation of coagulation. In DIC, there is a loss of balance between thrombin activation of coagulation and plasmin degradation of blot clots. Vascular or microvascular fibrin deposition as a result can compromise the blood supply to various organs, which can contribute to organ failure. Prolonged activation of the coagulation system impairs the synthesis of new coagulation factors and increases the degradation of existing coagulation factors, thus leading to decreased levels of procoagulant proteins. As a result, patients with DIC are at an increased risk of serious bleeding, especially during surgery and trauma situations. In acute, massive DIC, thrombocytopenia and depletion of coagulation factors, which promote severe bleeding, are accompanied by secondary fibrinolysis, wherein fibrin degradation products are generated that interfere with normal platelet function and impairs proper fibrin formation. The fibrinolysis is associated with high levels of plasmin which also contributes to the hemorrhagic state by degradation of coagulation factors, such as FIX, FVII, and FV. Treatments for acute DIC, therefore, aid in correcting the coagulation factor deficiencies in order to restore normal coagulation. In sub-acute or chronic DIC, patients present with a more hypercoagulatory phenotype, with thromboses from excess thrombin formation, and the symptoms and signs of venous thrombosis can be present. In contrast to acute DIC, sub-acute or chronic DIC is treated by methods of alleviating the hyperthrombosis, including heparin, anti-thrombin III and activated protein C treatment.

The modified FIX polypeptides provided herein and the nucleic acids encoding the modified FIX polypeptides provided herein can be used in therapies for acute DIC. In one embodiment, the modified FIX polypeptides herein, and nucleic acids encoding modified FIX polypeptides can be used in combination with other coagulation factors to treat deficiencies in clotting factors caused by acute DIC. The modified FIX polypeptides herein provide increased protein stability and increased protein half-life. Of particular interest are FIX polypeptides that are resistant to proteases. Thus, modified FIX polypeptides can be used to deliver longer lasting, more stable therapies for DIC. Examples of therapeutic improvements using modified FIX polypeptides include for example, but are not limited to, lower dosages, fewer and/or less frequent administrations, decreased side effects, and increased therapeutic effects. Modified FIX polypeptides can be tested for therapeutic effectiveness, for example, by using animal models. For example FIX-deficient mice, or any other known disease model for DIC, can be treated with modified FIX polypeptides. Progression of disease symptoms and phenotypes is monitored to assess the effects of the modified FIX polypeptides. Modified FIX polypeptides also can be administered to animal models as well as subjects such as in clinical trials to assess in vivo effectiveness in comparison to placebo controls and/or controls using unmodified FIX.

b. Bacterial Infection and Periodontitis

Systemic infection with microorganisms, such as bacteria, are commonly associated with DIC. The upregulation of coagulation pathways can be mediated in part by cell membrane components of the microorganism (lipopolysaccharide or endotoxin) or bacterial exotoxins (such as staphylococcal alpha toxin) that cause inflammatory responses leading to elevated levels of cytokines. The cytokines, in turn, can influence induction of coagulation.

Bacterial pathogens, such as Porphyrus gingivalis, are well-known as causative agents for adult periodontitis. The Porphyrus gingivalis bacterium produces arginine-specific cysteine proteinases that function as virulence factors (Grenier et al. (1987) J. Clin. Microbiol. 25:738-740, Smalley et al. (1989) Oral Microbiol. Immunol. 4:178-181, Marsh, et al. (1989) FEMS Microbiol. 59:181-185, and Potempa et al. (1998) J. Biol. Chem. 273:21648-21657. Porphyrus gingivalis generated two proteinases that are referred to as 50 kDa and 95 kDa gingipains R (RgpB and HRgpA, respectively). The protease can proteolytically cleave and hence activate coagulation factors, such as FIX. During bacterial infection release of the gingipains R into the blood stream can thus lead to uncontrolled activation of the coagulation cascade leading to overproduction of thrombin and increase the possibility of inducing disseminated intravascular coagulation (DIC). The large increases in thrombin concentrations can furthermore contribute alveolar bone resorption by osteoclasts at sites of periodontitis.

The modified FIX polypeptides provided herein that inhibit blood coagulation, and nucleic acids encoding modified FIX polypeptides can be used in treatment of periodontitis. The modified FIX polypeptides herein provide increased protein stability and improved half-life. Thus, modified FIX polypeptides can be used to deliver longer lasting, more stable therapies. Examples of therapeutic improvements using modified FIX polypeptides include, for example, but are not limited to, lower dosages, fewer and/or less frequent administrations, decreased side effects and increased therapeutic effects. Modified FIX polypeptides can be tested for therapeutic effectiveness for airway responsiveness in periodontitis models. Such models are available in animals, such as nonhuman primates, dogs, mice, rats, hamsters, and guinea pigs (Weinberg and Bral (1999) J. of Periodontology 26(6), 335-340). Modified FIX polypeptides also can be administered to animal models as well as subjects such as in clinical trials to assess in vivo effectiveness in comparison to placebo controls and/or controls using unmodified FIX.

c. Liver Disease

The liver is the site of production of most coagulation factors of the coagulation cascade. It also is responsible for clearing degraded and inactivated components of coagulation. As such, diseases of the liver can have a profound effect on hemostasis. In some cases, liver disease can be associated with hypersplenism and suppression of platelet production in the bone marrow. Liver disease can be characterized as either an acute or chronic condition. Acute hepatic necrosis is caused by factors, such as infection, shock, or toxins, wherein the necrosis of the liver leads to the inability to produce sufficient quantities of coagulation factors. Chronic liver disease is caused by factors, such as, but not limited to, alcohol, viral infection and autoimmune disease. Hemostatic defects in chronic liver disease include decreased coagulation factors due to decreased production, decreased platelet count due to sequestration in the spleen, and increased fibrin degradation products (FDP) due to decreased clearance, which can lead to conditions, such as DIC, as described above.

The modified FIX polypeptides provided herein and the nucleic acids encoding the modified FIX polypeptides provided herein can be used in therapies for liver disease, including treatment of deficiencies in coagulation factors. The modified FIX polypeptides provided herein can be used, for example, to control or prevent spontaneous bleeding episodes or to control or prevent bleeding in response to trauma or surgical procedures. The modified FIX polypeptides herein provide increased protein stability and increased protein half-life. Of particular interest are FIX polypeptides that are resistant to proteases. Thus, modified FIX polypeptides can be used to deliver longer lasting, more stable therapies for liver disease. Examples of therapeutic improvements using modified FIX polypeptides include for example, but are not limited to, lower dosages, fewer and/or less frequent administrations, decreased side effects, and increased therapeutic effects. Modified FIX polypeptides can be tested for therapeutic effectiveness, for example, by using animal models. For example animal models of autoimmune liver disease and alcohol induced liver disease are available and can be treated with modified FIX polypeptides provided herein (such as Nanji et al. (2003) Alcohol Res Health. 27(4):325-30; Heneghan and McFarlane (2005) Hepatology 42(1): 149-55). Progression of disease symptoms and phenotypes is monitored to assess the effects of the modified FIX polypeptides. Modified FIX polypeptides also can be administered to animal models as well as subjects such as in clinical trials to assess in vivo effectiveness in comparison to placebo controls and/or controls using unmodified FIX.

d. Warfarin and Heparin-Induced Bleeding

Patients undergoing anticoagulant therapies for the treatment of conditions, such as thromboembolism, can exhibit bleeding episodes upon acute administration of anticoagulants or develop hemorrhagic disorders as a result long term usage of such therapies. Treatments for bleeding episodes typically include administration of procoagulants, such as vitamin K, plasma, concentrates of FIX polypeptides, and protamines to neutralize heparin. The modified FIX polypeptides provided herein can be used in treatments to control bleeding episodes in patients with acquired bleeding disorders due to anticoagulant treatments.

e. Intracerebral Hemorrhage

Intracerebral hemorrhage (ICH) is a type of stroke characterized by spontaneous bleeding into the brain. In contrast to ischemic stroke, which can be treated effectively with anticoagulant therapies, the progressive bleeding induced in ICH is more difficult to treat. Mortality from hemorrhagic stroke at 30 days is seven times higher than ischemic strokes. The most common cause of ICH is degeneration and rupture of small arteries or arterioles due to sustained hypertension. In the elderly, cerebral amyloid angiopathy also can induce ICH Therapies for ICH involves the use of coagulation factor therapies, in particular recombinant factor VII. The modified FIX polypeptides provided herein, either alone or in combination with other coagulation factors, can be used in treatments to control bleeding episodes in patients with ICH.

J. COMBINATION THERAPIES

Any of the modified FIX polypeptides, and nucleic acid molecules encoding modified FIX polypeptides described herein can be administered in combination with, prior to, intermittently with, or subsequent to, other therapeutic agents or procedures including, but not limited to, other biologics, small molecule compounds and surgery. For any disease or condition, including all those exemplified above, for FIX is indicated or has been used and for which other agents and treatments are available, FIX can be used in combination therewith. Hence, the modified FIX polypeptides provided herein similarly can be used. Depending on the disease or condition to be treated, exemplary combinations include, but are not limited to combination with other plasma purified or recombinant coagulation factors, procoagulants, anticoagulants, anti-coagulation antibodies, glycosaminoglycans, heparins, heparinoids, heparin derivatives, heparin-like drugs, coumarins, such as warfarin and coumarin derivatives. Additional procoagulants that can be used in combination therapies with modified FIX polypeptides include, but are not limited to, vitamin K, vitamin K derivatives, and protein C inhibitors. Additional anticoagulants that can be used in combination therapies with modified FIX polypeptides include, but are not limited to, β2 adrenoreceptor antagonists, neuropeptide V2 antagonists, prostacyclin analogs, thromboxane synthase inhibitors, calcium agonists, elastase inhibitors, non-steroidal anti-inflammatory molecules, thrombin inhibitors, lipoxygenase inhibitors, FVIIa inhibitors, FXa inhibitors, phosphodiesterase III inhibitors, fibrinogen, vitamin K antagonists, and glucoprotein IIb/IIIa antagonists.

K. ARTICLES OF MANUFACTURE AND KITS

Pharmaceutical compounds of modified FIX polypeptides for nucleic acids encoding modified FIX polypeptides, or a derivative or a biologically active portion thereof can be packaged as articles of manufacture containing packaging material, a pharmaceutical composition which is effective for treating a FIX-mediated disease or disorder, and a label that indicates that modified FIX polypeptide or nucleic acid molecule is to be used for treating a FIX-mediated disease or disorder.

The articles of manufacture provided herein contain packaging materials. Packaging materials for use in packaging pharmaceutical products are well known to those of skill in the art. See, for example, U.S. Pat. Nos. 5,323,907, 5,033,252 and 5,052,558, each of which is incorporated herein in its entirety. Examples of pharmaceutical packaging materials include, but are not limited to, blister packs, bottles, tubes, inhalers, pumps, bags, vials, containers, syringes, bottles, and any packaging material suitable for a selected formulation and intended mode of administration and treatment. A wide array of formulations of the compounds and compositions provided herein are contemplated as are a variety of treatments for any FIX-mediated disease or disorder.

Modified FIX polypeptides and nucleic acid molecules also can be provided as kits. Kits can include a pharmaceutical composition described herein and an item for administration. For example a modified FIX can be supplied with a device for administration, such as a syringe, an inhaler, a dosage cup, a dropper, or an applicator. The kit can, optionally, include instructions for application including dosages, dosing regimens and instructions for modes of administration. Kits also can include a pharmaceutical composition described herein and an item for diagnosis. For example, such kits can include an item for measuring the concentration, amount or activity of FIX or a FIX regulated system of a subject.

L. EXAMPLES

The following examples are included for illustrative purposes only and are not intended to limit the scope of the embodiments provided herein.

Example 1 Cloning and Generation FIX Mutants

A. Cloning of cDNA Encoding FIX and Insertion into a Mammalian Expression Vector

The nucleotide sequence comprising the coding sequence of FIX was cloned into the plasmid pCR-Blunt II-TOPO (Invitrogen, SEQ ID NO: 915) by polymerase chain reaction (PCR), using standard techniques known in the art, from plasmid pCMV5.8 (ATCC Number: 79829), using the following primers:

FIXHIND 5′-GCATTAGGATAAGCTTGGATGCAGCGCGTGAACATG-3′ (SEQ ID NO: 913) and

FIXXBA 5′-GCATCGGCGCAGATCTCTGTTAATTTTCAATTCC-3′ (SEQ ID NO: 914). After confirming the sequence of the FIX fragment contained in the pTOPO-PCR bluntII plasmid by sequencing, the FIX fragment was subcloned by restriction digest using EcoRI into plasmid pNaut to produce plasmid pNaut-FIX-EcoRI (SEQ ID NO: 916). The encoded mature form of the FIX polypeptide has a sequence of amino acids as set forth in SEQ ID NO: 1035. This sequence differs from SEQ ID NO: 2 at five positions: K39T, L40E, 143K, S44Q and S46V. These changes do not affect the clotting activity of the polypeptide.

B. Generation of FIX Mutants

A collection of pre-designed, targeted mutants was generated such that each individual mutant was created and processed individually, and physically separated from each other and in addressable arrays. 2D-scanning technology, described herein and also described in published U.S. Application Nos. US-2004-0132977-A1 and US 2005-0202438 A1) was used to design and obtain FIX mutants with improved resistance to proteolysis. Is-HITs were identified based upon (1) the protein property to be evolved (such as, resistance to proteolysis or stability); (2) the amino acid sequence; and (3) the properties of individual amino acids.

1. LEADS Created for Higher Resistance to Proteolysis of FIX

Variants were designed using 2D-scanning to identify positions conferring resistance to proteolysis. Positions selected (is-HITs) on human FIX (SEQ ID NO: 2) were (numbering corresponds to amino acid positions in the mature FIX polypeptide set forth in SEQ ID NO: 2) Y1, S3, G4, K5, L6, E7, E8, F9, V10, G12, L14, E15, R16, E17, M19, E20, E21, K22, S24, F25, E26, E27, A28, R29, E30, V31, F32, E33, T35, E36, R37, T38, T39, E40, F41, W42, K43, Y45, V46, D47, G48, D49, E52, S53, P55, L57, N58, G59, G60, S61, K63, D64, D65, 166, S68, Y69, E70, W72, P74, F75, G76, F77, E78, G79, K80, E83, L84, D85, V86, T87, I90, K91, N92, G93, R94, E96, F98, K100, S102, A103, D104, K106, V107, V108, S110, T112, E113, G114, Y115, R116, L117, A118, E119, K122, S123, E125, P126, A127, V128, P129, P131, G133, R134, V135, S136, V137, S138, T140, S141, K142, L143, T144, R145, A146, E147, T148, V149, P151, D152, V153, D154, Y155, V156, S158, T159, E160, A161, E162, T163, I164, L165, D166, I168, T169, S171, T172, S174, F175, D177, F178, T179, R180, V181, V182, G183, G184, E185, D186, A187, K188, P189, G190, F192, P193, W194, V196, V197, L198, N199, G200, K201, V202, D203, A204, F205, G207, G208, S209, I210, V211, E213, K214, W215, I216, V217, T218, A219, A220, V223, E224, T225, G226, V227, K228, I229, T230, V231, V232, A233, G234, E235, I238, E239, E240, T241, E242, T244, E245, K247, R248, V250, I251, R252, I253, I254, P255, Y259, A261, A262, I263, K265, Y266, D269, I270, A271, L272, L273, E274, L275, D276, E277, P278, L279, V280, L281, S283, Y284, V285, T286, P287, I288, 1290, A291, D292, K293, E294, Y295, T296, I298, F299, L300, K301, F302, G303, S304, G305, Y306, V307, S308, G309, W310, G311, R312, V313, F314, K316, G317, R318, S319, A320, L321, V322, L323, Y325, L326, I327, V328, P329, L330, V331, D332, R333, A334, T335, L337, R338, S339, T340, K341, F342, T343, I344, Y345, M348, F349, A351, G352, F353, E355, G356, G357, R358, D359, S360, G363, D364, S365, G366, G367, P368, V370, T371, E372, V373, E374, G375, T376, S377, F378, L379, T380, G381, I382, I383, S384, W385, G386, E387, E388, A390, M391, K392, G393, K394, Y395, G396, I397, Y398, T399, K400, V401, S402, R403, Y404, V405, W407, I408, K409, E410, K411, T412, K413, L414, and T415. The native amino acid at each of the is-HIT positions listed above was replaced by residues as listed in Table 9.

TABLE 9 Amino acid at Replacing is-HIT ammo acids R H, Q E H, N, Q K N, Q D N, Q M I, V P A, S Y I, H F I, V W H, S L I, V N Q, S A H, N, Q G H, N, Q I H, N, Q S H, N, Q T H, N, Q V H, N, Q

The FIX variants generated for testing increased resistance to proteolysis are listed in Table 10 (SEQ ID NOS: 3-891, 1025-1034, 1036-1926, and 2035-2044).

TABLE 10 List of human FIX variants for testing increased resistance to proteolysis Y1H Y1I S3Q S3H S3N G4Q G4H G4N K5N K5Q L6I L6V E7Q E7H E7N E8Q E8H E8N F9I F9V V10Q V10H V10N G12Q G12H G12N L14I L14V E15Q E15H E15N R16H R16Q E17Q E17H E17N M19I M19V E20Q E20H E20N E21Q E21H E21N K22N K22Q S24Q S24H S24N F25I F25V E26Q E26H E26N E27Q E27H E27N A28Q A28H A28N R29H R29Q E30Q E30H E30N V31Q V31H V31N F32I F32V E33Q E33H E33N T35Q T35H T35N E36Q E36H E36N R37H R37Q T38Q T38H T38N T39Q T39H T39N E40Q E40H E40N F41I F41V W42S W42H K43N K43Q Y45H Y45I V46Q V46H V46N D47N D47Q G48Q G48H G48N D49N D49Q E52Q E52H E52N S53Q S53H S53N P55A P55S L57I L57V N58Q N58S G59Q G59H G59N G60Q G60H G60N S61Q S61H S61N K63N K63Q D64N D64Q D65N D65Q I66Q I66H I66N S68Q S68H S68N Y69H Y69I E70Q E70H E70N W72S W72H P74A P74S F75I F75V G76Q G76H G76N F77I F77V E78Q E78H E78N G79Q G79H G79N K80N K80Q E83Q E83H E83N L84I L84V D85N D85Q V86Q V86H V86N T87Q T87H T87N I90Q I90H I90N K91N K91Q N92Q N92S G93Q G93H G93N R94H R94Q E96Q E96H E96N F98I F98V K100N K100Q S102Q S102H S102N A103Q A103H A103N D104N D104Q K106N K106Q V107Q V107H V107N V108Q V108H V108N S110Q S110H S110N T112Q T112H T112N E113Q E113H E113N G114Q G114H G114N Y115H Y115I R116H R116Q L117I L117V A118Q A118H A118N E119Q E119H E119N K122N K122Q S123Q S123H S123N E125Q E125H E125N P126A P126S A127Q A127H A127N V128Q V128H V128N P129A P129S P131A P131S G133Q G133H G133N R134H R134Q V135Q V135H V135N S136Q S136H S136N V137Q V137H V137N S138Q S138H S138N T140Q T140H T140N S141Q S141H S141N K142N K142Q L143I L143V T144Q T144H T144N R145H R145Q A146Q A146H A146N E147Q E147H E147N T148Q T148H T148N V149Q V149H V149N P151A P151S D152N D152Q V153Q V153H V153N D154N D154Q Y155H Y155I V156Q V156H V156N S158Q S158H S158N T159Q T159H T159N E160Q E160H E160N A161Q A161H A161N E162Q E162H E162N T163Q T163H T163N I164Q I164H I164N L165I L165V L165Q L165H D166N D166Q I168Q I168H I168N T169Q T169H T169N S171Q S171H S171N T172Q T172H T172N S174Q S174H S174N F175I F175V F175H D177N D177Q F178I F178V F178H T179Q T179H T179N R180H R180Q V181Q V181H V181N V182Q V182H V182N G183Q G183H G183N G184Q G184H G184N E185Q E185H E185N D186N D186Q A187Q A187H A187N K188N K188Q P189A P189S G190Q G190H G190N F192I F192V F192IH P193A P193S W194S W194H W194I V196Q V196H V196N V197Q V197H V197N L198I L198V L198Q L198H N199Q N199S G200Q G200H G200N K201N K201Q V202Q V202H V202N D203N D203Q A204Q A204H A204N F205I F205V G207Q G207H G207N G208Q G208H G208N S209Q S209H S209N I210Q I210H I210N V211Q V211H V211N E213Q E213H E213N K214N K214Q W215S W215H I216Q I216H I216N V217Q V217H V217N T218Q T218H T218N A219Q A219H A219N A220Q A220H A220N V223Q V223H V223N E224Q E224H E224N T225Q T225H T225N G226Q G226H G226N V227Q V227H V227N K228N K228Q I229Q I229H I229N T230Q T230H T230N V231Q V231H V231N V232Q V232H V232N A233Q A233H A233N G234Q G234H G234N E235Q E235H E235N I238Q I238H I238N E239Q E239H E239N E240Q E240H E240N T241Q T241H T241N E242Q E242H E242N T244Q T244H T244N E245Q E245H E245N K247N K247Q R248H R248Q V250Q V250H V250N I251Q I251H I251N R252H R252Q I253Q I253H I253N I254Q I254H I254N P255A P255S Y259H Y259I A261Q A261H A261N A262Q A262H A262N I263Q I263H I263N K265N K265Q Y266H Y266I D269N D269Q I270Q I270H I270N A271Q A271H A271N L272I L272V L273I L273V E274Q E274H E274N L275I L275V D276N D276Q E277Q E277H E277N P278A P278S L279I L279V V280Q V280H V280N L281I L281V S283Q S283H S283N Y284H Y284I V285Q V285H V285N T286Q T286H T286N P287A P287S I288Q I288H I288N I290Q I290H I290N A291Q A291H A291N D292N D292Q K293N K293Q E294Q E294H E294N Y295H Y295I T296Q T296H T296N I298Q I298H I298N F299I F299V L300I L300V K301N K301Q F302I F302V G303Q G303H G303N S304Q S304H S304N G305Q G305H G305N Y306H Y306I V307Q V307H V307N S308Q S308H S308N G309Q G309H G309N W310S W310H G311Q G311H G311N R312H R312Q V313Q V313H V313N F314I F314V K316N K316Q G317Q G317H G317N R318H R318Q S319Q S319H S319N A320Q A320H A320N L321I L321V V322Q V322H V322N L323I L323V Y325H Y325I L326I L326V R327H R327Q V328Q V328H V328N P329A P329S L330I L330V V331Q V331H V331N D332N D332Q R333H R333Q A334Q A334H A334N T335Q T335H T335N L337I L337V R338H R338Q S339Q S339H S339N T340Q T340H T340N K341N K341Q F342I F342V T343Q T343H T343N I344Q I344H I344N Y345H Y345I M348I M348V F349I F349V A351Q A351H A351N G352Q G352H G352N F353I F353V E355Q E355H E355N G356Q G356H G356N G357Q G357H G357N R358H R358Q D359N D359Q S360Q S360H S360N G363Q G363H G363N D364N D364Q S365Q S365H S365N G366Q G366H G366N G367Q G367H G367N P368A P368S V370Q V370H V370N T371Q T371H T371N E372Q E372H E372N V373Q V373H V373N E374Q E374H E374N G375Q G375H G375N T376Q T376H T376N S377Q S377H S377N F378I F378V L379I L379V T380Q T380H T380N G381Q G381H G381N I382Q I382H I382N I383Q I383H I383N S384Q S384H S384N W385S W385H G386Q G386H G386N E387Q E387H E387N E388Q E388H E388N A390Q A390H A390N M391I M391V K392N K392Q G393Q G393H G393N K394N K394Q Y395H Y395I G396Q G396H G396N I397Q I397H I397N Y398H Y398I T399Q T399H T399N K400N K400Q V401Q V401H V401N S402Q S402H S402N R403H R403Q Y404H Y404I V405Q V405H V405N W407S W407H I408Q I408H I408N K409N K409Q E410Q E410H E410N K411N K411Q T412Q T412H T412N K413N K413Q L414I L414V T415Q T415H T415N

Example 2 Production of Native and Modified Human FIX Polypeptides (Proteins) in Mammalian Cells and Yield Determination

Human fetal kidney 293 HEK EBNA fibroblast cells were grown in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 2 mM glutamine and 10% SVF. Cells were plated at 5×10⁵ cells per well in 6-well plate for 2 days, washed two times with PBS, and then switched to serum free medium. Cells were transfected with 2 μg of DNA (FIX variants in pNaut-FIX plasmid) using transfection reagent according to the instructions of the manufacturer (Perfectin, GTS). Cell medium was replaced after 4 hours with serum free media containing 50 μg/ml of vitamin K and 1×-ITS (insulin, transferrin, selenium) mixture. Cell medium was collected 72 hours after transfection and stored at −80° C.

ASSERACHROM® IX: Ag ELISA (Diagnostica Stago, France) was used to determine concentration of FIX in supernatants from cell production according to the instructions of the manufacturer. Samples were diluted 20-fold using kit dilution reagent. Absorbance at 492 nm was measured using a spectrophotometer (Spectramax, Molecular Devices). Results were obtained by interpolation of the absorbance values from the calibration curve obtained from patients' plasma dilutions and plotted in log-log graph. FIX level at 100% corresponded approximately to 4 mg/l. Yields of FIX native and mutant proteins produced in 293 HEK cells are shown in Table 11. The data are the results from two productions.

TABLE 11 Yield of FIX native and mutant proteins Nemo Code # Mutation FIX (mg/L) 1 Native FIX 9.2 2 T163N 14.1 3 T163Q 11.2 4 T163H 10.1 5 I164N 8.9 6 I164Q 13.3 7 I164H 14.9 8 T163N/I164N 10.6 9 I168N 11.9 10 I168Q 11.9 11 I168H 12.6 12 T169N 7.5 13 T169Q 9.1 14 T169H 9.7 15 S171N 11.3 16 S171Q 11.7 17 S171H 10.2 18 T172N 17.9 19 T172Q 12.6 20 T172H 16.3 21 S174N 14.3 22 S174Q 11.5 23 S174H 12.1 24 I168N/T169N/S171N/T172N/S174N 12.9 25 T179N 10.0 26 T179Q 13.3 27 T179H 8.3 28 V181N 9.8 29 V181Q 20.3 30 V181H 13.2 31 V182N 7.5 32 V182Q 7.6 33 V182H 12.1 34 G183N 14.1 35 G183Q 15.4 36 G183H 11.6 37 G184N 7.6 38 G184Q 10.7 39 G184H 8.9 40 T179N/V181N/V182N/G183N/G184N 4.9 41 A187N 1.3 42 A187Q 3.0 43 A187H 1.6 44 G190N 1.1 45 G190Q 0.4 46 G190H 5.4 47 A187N/G190N 1.1 48 V196N 0.5 49 V196Q 0.1 50 V196H 0.1 51 V197N 0.6 52 V197Q 1.4 53 V197H 3.1 54 V196N/V197N 0.1 55 R180H 9.9 56 R180Q 8.1 57 K188N 10.5 58 K188Q 13.4 59 K201N 8.3 60 K201Q 6.7 61 L165I 7.0 62 L165V 11.3 63 F175I 7.0 64 F175V 9.3 65 F178I 10.3 66 F178V 8.7 67 F192I 2.9 68 F192V 1.7 69 W194H 0.1 70 W194I 0.1 71 L198I 6.5 72 L198V 9.8 73 D166Q 7.6 74 D166N 6.8 75 D177Q 8.4 76 D177N 7.7 77 D186Q 9.7 78 D186N 14.6 79 D203Q 4.5 80 D203N 1.0 81 T140N 12.9 82 T140Q 11.4 83 T140H 7.8 84 T144N 9.3 85 T144Q 1.8 86 T144H 9.3 87 T140N/T144N 6.3 88 L165Q 13.9 89 L165H 8.3 90 F175L/F178I 8.1 91 F175H 10.7 92 F178H 4.5 93 F192I/W194I <0.1 94 F192H 0.8 95 L198Q 0.1 96 L198H 1.5 97 D152N/D154N 7.2 98 D152N 11.8 99 D152Q 7.0 100 D154N 4.4 101 D154Q 6.7

Example 3 Determination of Specific Activity of Human FIX by Coagulation Assay

The collection of human FIX mutants was tested for coagulation activity. Coagulation activity (expressed as clotting time T₅₀) was determined as the concentration needed for formation of a fibrin clot. Clotting activity of native and mutant FIX molecules was measured by the one stage activated partial thromboplastin time (aPTT) clotting assay (Cephascreen, Diagnostica Stago, France) using FIX immunodepleted human plasma (Deficient IX, Diagnostica Stago, France).

Briefly, 20 μl of production supernatant containing 60 ng of native FIX or mutant FIX was diluted with 60 μl of immunodepleted plasma. 80 μl of Cephascreen reagent containing cephalin (platelet substitute) prepared from rabbit cerebral tissues and a polyphenolic activator in a buffered medium was added to diluted FIX samples and incubated at 37° C. for 15 minutes. 80 μl of pre-warmed CaCl₂ (0.025M, Diagnostica Stago, France) was added to mixture of FIX/Cephascreen reagent samples, and the time required for clot formation was immediately monitored using spectrophotometer (Spectramax, Molecular devices) at 350 nm. Serial dilution of normal human pooled plasma representing 100 to 120% of FIX activity (System control N, Diagnostica Stago, France) was used as the standard curve in order to validate linearity of clotting time detection. Clotting activity of FIX native and mutant proteins by clotting assay is shown in Tables 12a and 12b. The T₅₀ values are displayed in seconds and represent the time required to achieved 50% clotting. The data are the result from two assays done in duplicate. Tables 12a and 12b below depict two separate experiments measuring the coagulation activity of exemplary non-limiting modified FIX polypeptides and native FIX. Table 12c depicts the protease specificity groups as indicated for each mutant.

TABLE 12a Clotting activity of FIX native and mutant proteins Bioactivity Nemo Clotting Assay Code # Mutation T50 (sec) 1 Native FIX 116 2 T163N 111 3 T163Q 117 4 T163H 108 5 I164N 105 6 I164Q 113 7 I164H 118 8 T163N/I164N 108 9 I168N 112 10 I168Q 119 11 I168H 112 12 T169N 104 13 T169Q 104 14 T169H 111 15 S171N 116 16 S171Q 112 17 S171H 110 18 T172N 133 19 T172Q 111 20 T172H 111 21 S174N 113 22 S174Q 115 23 S174H 113 24 I168N/T169N/S171N/T172N/S174N 112 25 T179N 115 26 T179Q 112 27 T179H 110 28 V181N 178 29 V181Q 141 30 V181H 179 31 V182N 174 32 V182Q 156 33 V182H 176 34 G183N 146 35 G183Q 155 36 G183H 170 37 G184N 177 38 G184Q 178 39 G184H 179 40 T179N/V181N/V182N/G183N/G184N nd 41 A187N 180 42 A187Q 169 43 A187H 201 44 G190N 148 45 G190Q 162 46 G190H 120 47 A187N/G190N 194 48 V196N 183 49 V196Q 176 50 V196H 183 51 V197N 161 52 V197Q 157 53 V197H 123 54 V196N/V197N 190 55 R180H 191 56 R180Q 186 57 K188N 124 58 K188Q 130 59 K201N 119 60 K201Q 118 61 L165I 109 62 L165V 120 63 F175I 116 64 F175V 118 65 F178I 140 66 F178V 122 67 F192I 134 68 F192V 145 69 W194H 183 70 W194I 168 71 L198I 124 72 L198V 168 73 D166Q 119 74 D166N 118 75 D177Q 118 76 D177N 182 77 D186Q 127 78 D186N 117 79 D203Q 109 80 D203N 113 81 T140N 118 82 T140Q 143 83 T140H 119 84 T144N 151 85 T144Q nd 86 T144H 117 87 T140N/T144N 133 88 L165Q 117 89 L165H 118 90 F175I/F178I 155 91 F175H 153 92 F178H 127 93 F192I/W194I 175 94 F192H 154 95 L198Q 183 96 L198H 178 97 D152N/D154N 125 98 D152N 148 99 D152Q 126 100 D154N 119 101 D154Q 150 nd = not determined

TABLE 12b Clotting activity of FIX native and mutant proteins Bioactivity Nemo Clotting Assay Code # Mutation T50 (sec) 1 Native FIX 114 2 T163N 113 3 T163Q 118 4 T163H 110 5 I164N 107 6 I164Q 114 7 I164H 115 8 T163N/I164N 110 9 I168N 111 10 I168Q 119 11 I168H 111 12 T169N 110 13 T169Q 108 14 T169H 111 15 S171N 116 16 S171Q 111 17 S171H 110 18 T172N 143 19 T172Q 112 20 T172H 113 21 S174N 113 22 S174Q 115 23 S174H 112 24 I168N/T169N/S171N/T172N/S174N 113 25 T179N 116 26 T179Q 114 27 T179H 115 28 V181N 200 29 V181Q 120 30 V181H 196 31 V182N 180 32 V182Q 165 33 V182H 180 34 G183N 150 35 G183Q 162 36 G183H 182 37 G184N 195 38 G184Q 187 39 G184H 192 40 T179N/V181N/V182N/G183N/G184N 169 41 A187N 200 42 A187Q 163 43 A187H 202 44 G190N 148 45 G190Q 158 46 G190H 123 47 A187N/G190N 201 48 V196N 191 49 V196Q 183 50 V196H 191 51 V197N 155 52 V197Q 148 53 V197H 130 54 V196N/V197N 203 55 R180H 202 56 R180Q 200 57 K188N 124 58 K188Q 130 59 K201N 121 60 K201Q 118 61 L165I 109 62 L165V 121 63 F175I 119 64 F175V 120 65 F178I 166 66 F178V 122 67 F192I 113 68 F192V 134 69 W194H 192 70 W194I 188 71 L1981 128 72 L198V 175 73 D166Q 118 74 D166N 116 75 D177Q 118 76 D177N 195 77 D186Q 125 78 D186N 116 79 D203Q 112 80 D203N 110 81 T140N 116 82 T140Q 124 83 T140H 117 84 T144N 132 85 T144Q 123 86 T144H 114 87 T140N/T144N 128 88 L165Q 117 89 L165H 119 90 F175I/F178I 147 91 F175H 131 92 F178H 122 93 F192I/W194I 193 94 F192H 154 95 L198Q 198 96 L198H 199 97 D152N/D154N 121 98 D152N 131 99 D152Q 121 100 D154N 112 101 D154Q 134 102 D152N 123 103 D152Q 121 104 D154N 120 105 D154Q 118

TABLE 12c Protease specificity groups for FIX mutant proteins Nemo Specificity Code # Mutation Group 1 Native FIX — 2 T163N E 3 T163Q E 4 T163H E 5 I164N E 6 I164Q E 7 I164H E 8 T163N/I164N E 9 I168N E 10 I168Q E 11 I168H E 12 T169N E 13 T169Q E 14 T169H E 15 S171N E 16 S171Q E 17 S171H E 18 T172N E 19 T172Q E 20 T172H E 21 S174N E 22 S174Q E 23 S174H E 24 I168N/T169N/S171N/T172N/S174N E 25 T179N E 26 T179Q E 27 T179H E 28 V181N E 29 V181Q E 30 V181H E 31 V182N E 32 V182Q E 33 V182H E 34 G183N E 35 G183Q E 36 G183H E 37 G184N E 38 G184Q E 39 G184H E 40 T179N/V181N/V182N/G183N/G184N E 41 A187N E 42 A187Q E 43 A187H E 44 G190N E 45 G190Q E 46 G190H E 47 A187N/G190N E 48 V196N E 49 V196Q E 50 V196H E E 51 V197N E 52 V197Q E 53 V197H E 54 V196N/V197N E 55 R180H T 56 R180Q T 57 K188N T 58 K188Q T 59 K201N T 60 K201Q T 61 L165I CT 62 L165V CT 63 F175I CT 64 F175V CT 65 F178I CT 66 F178V CT 67 F192I CT 68 F192V CT 69 W194H CT 70 W194I CT 71 L198I CT 72 L198V CT 73 D166Q EAsp 74 D166N EAsp 75 D177Q EAsp 76 D177N EAsp 77 D186Q EAsp 78 D186N EAsp 79 D203Q EAsp 80 D203N EAsp 81 T140N CT 82 T140Q CT 83 T140H CT 84 T144N CT 85 T144Q CT 86 T144H CT 87 T140N/T144N CT 88 L165Q CT 89 L165H CT 90 F175I/F178I CT 91 F175H CT 92 F178H CT 93 F192I/W194I CT 94 F192H CT 95 L198Q CT 96 L198H CT 97 D152N/D154N EAsp 98 D152N EAsp 99 D152Q EAsp 100 D154N EAsp 101 D154Q EAsp 102 D152N EAsp 103 D152Q EAsp 104 D154N EAsp 105 D154Q EAsp E = elastase; T = trypsin; CT = chymotrypsin; EAsp = Endoproteinase AspN

Example 4 Resistance to Proteolysis

The collection of human FIX mutants was tested for their resistance to proteolysis as measured by retention of coagulation activity following treatment with proteases. Equal amounts of FIX native or mutant proteins (60 ng per assays) were treated with selected proteases (1.5% w/w trypsin, chymotrypsin, endoproteinase AspN, and endoproteinase GluC; and 6% w/w elastase). Aliquots of the samples were taken at different time points between 0.083 and 8 hrs and the proteolysis reaction was stopped by adding antiprotease cocktail (Roche Cat No. 11836170001). Samples were conserved at −20° C. until determination of clotting time could be performed. Clotting activity of the treated samples was assayed as described in Example 3 to determine residual clotting activity at each time point. Resistance to proteases for exemplary non-limiting modified FIX polypeptides is displayed in Table 13 as either no change in (N) or increased (+) resistance to proteases as compared to the residual coagulation activity of native FIX under the same protease treatment conditions.

The data are not meant to be representative of all proteases, but are exemplary data showing the resistance to proteolysis to an exemplary protease cocktail containing the proteases as described above. Thus, the data are not comprehensive and are not meant to be indicative that other FIX polypeptides do not exhibit protease resistance.

TABLE 13 Resistance to proteolysis of FIX native and mutant proteins Nemo Resistance Code # Mutation to proteases 1 Native FIX — 2 T163N N 3 T163Q N 4 T163H + 5 I164N N 6 I164Q + 7 I164H + 8 T163N/I164N + 9 I168N N 10 I168Q + 11 I168H + 12 T169N N 13 T169Q N 14 T169H + 15 S171N + 16 S171Q + 17 S171H N 18 T172N N 19 T172Q + 20 T172H N 21 S174N N 22 S174Q + 23 S174H + 24 I168N/T169N/S171N/T172N/S174N N 25 T179N + 26 T179Q + 27 T179H + 28 V181N N 29 V181Q + 30 V181H N 31 V182N + 32 V182Q N 33 V182H N 34 G183N N 35 G183Q N 36 G183H N 37 G184N + 38 G184Q N 39 G184H N 40 T179N/V181N/V182N/G183N/G184N N 41 A187N N 42 A187Q + 43 A187H N 44 G190N N 45 G190Q N 46 G190H N 47 A187N/G190N N 48 V196N N 49 V196Q N 50 V196H N 51 V197N N 52 V197Q N 53 V197H + 54 V196N/V197N N 55 R180H N 56 R180Q N 57 K188N N 58 K188Q N 59 K201N N 60 K201Q N 61 L1651 N 62 L165V N 63 F175I N 64 F175V N 65 F178I N 66 F178V N 67 F192I + 68 F192V N 69 W194H N 70 W194I N 71 L198I + 72 L198V + 73 D166Q + 74 D166N + 75 D177Q + 76 D177N + 77 D186Q + 78 D186N + 79 D203Q + 80 D203N + 81 T140N N 82 T140Q N 83 T140H N 84 T144N N 85 T144Q N 86 T144H N 87 T140N/T144N + 88 L165Q N 89 L165H N 90 F175I/F178I + 91 F175H + 92 F178H N 93 F192I/W194I N 94 F192H N 95 L198Q N 96 L198H N 97 D152N/D154N + 98 D152N N 99 D152Q + 100 D154N + 101 D154Q N N = no change; + = Increased resistance to proteolysis

In one exemplary assay, native FIX had a large increase in its T₅₀ clotting time from about 140 seconds to about 200 seconds after only 0.5 hours of incubation with proteases, whereas exemplary modified FIX polypeptides with increased resistance to proteases, such as D203Q, had an increase in T₅₀ clotting time from about 150 seconds to about 160 seconds after 0.5 hours of incubation with proteases. After 2 hours of incubation with proteases the T₅₀ clotting time for D203Q only increased to about 173 seconds, and after 3 hours, 190 seconds. Similarly, exemplary modified FIX polypeptides D154N, and D152N/D154N exhibited T₅₀ clotting times of 160 seconds and 170 seconds, respectively, after 0.5 hours of incubation with proteases, and 170 seconds and 178 seconds, after 2 hours of incubation with proteases. The results demonstrate that exemplary modified FIX polypeptides are more resistant to protease treatment than native FIX. Thus, the modified FIX polypeptides indicated to have an “increase” protease resistance as compared to native FIX have a greater half-life and are more stable than wild-type FIX polypeptides following incubation with one or more proteases.

Example 5 SuperLEAD Clotting Activity and Resistance to Proteolysis

Based on the data obtained above for protease resistance of FIX LEAD polypeptides, selected FIX SuperLEAD polypeptides were generated and tested for their clotting activity and resistance to proteolysis as measured by retention of coagulation activity following treatment with proteases. A schematic representation of the combinations used to generate triple SuperLEADs is shown in Table 14.

TABLE 14 Generation of SuperLEAD Combinations 2^(nd) mutation NEMO code (Endoproteinase AspN) 67 73 74 77 78 79 80 97 100 ← 4 141 142 143 144 145 146 147 148 6 149 150 151 152 153 154 155 156 8 157 158 159 160 161 162 163 164 14 165 166 167 168 169 170 171 172 16 173 174 175 176 177 178 179 180 22 181 182 183 184 185 186 187 188 23 189 190 191 192 193 194 195 196 26 197 198 199 200 201 202 203 204 27 205 206 207 208 209 210 211 212 ↑ 3^(rd) mutation (Elastase)

Clotting activity of exemplary non-limiting FIX SuperLEAD polypeptides was assayed as described above in Example 3, and the data is shown in Table 14b. The T₅₀ values are displayed in seconds and represent the time required to achieved 50% clotting.

TABLE 14b Clotting activity of FIX SuperLEAD mutant proteins Bioactivity Nemo Clotting Assay Code # Mutation T₅₀ (sec) 107 T163H/F192I 99 108 I164Q/F192I 101 109 T163N/I164N/F192I 106 110 T169H/F192I 94 111 S171Q/F192I 105 112 S174Q/F192I 99 113 S174H/F192I 101 114 T179Q/F192I 94 115 T179H/F192I 101 116 D166Q/F192I 93 117 D166N/F192I 104 118 D186Q/F192I 113 119 D186N/F192I 111 120 F192I/D203Q 90 121 F192I/D203N 181 122 T148A/D152N/D154N/F192I 90 123 T148A/D154N/F192I 105 141 T163H/D166Q/F192I 97 142 T163H/D166N/F192I 89 143 T163H/D186Q/F192I 123 144 T163H/D186N/F192I 103 145 T163H/F192I/D203Q 90 146 T163H/F192I/D203N 89 147 T148A/D152N/D154N/T163H/F192I 101 148 T148A/D154N/T163H/F192I 92 149 I164Q/D166Q/F192I ND 150 I164Q/D166N/F192I ND 151 I164Q/D186Q/F192I 109 152 I164Q/D186N/F192I 101 153 I164Q/F192I/D203Q 96 154 I164Q/F192I/D203N 87 155 T148A/D152N/D154N/I164Q/F192I 97 156 T148A/D154N/I164Q/F192I 95 157 T163N/I164N/D166Q/F192I 103 158 T163N/I164N/D166N/F192I 100 159 T163N/I164N/D186Q/F192I 128 160 T163N/I164N/D186N/F192I 102 161 T163N/I164N/F192I/D203Q 101 162 T163N/I164N/F192I/D203N 95 163 T148A/D152N/D154N/T163N/I164N/F192I 100 164 T148A/D154N/T163N/I164N/F192I 97 165 D166Q/T169H/F192I 99 166 D166N/T169H/F192I 96 167 T169H/D186Q/F192I 114 168 T169H/D186N/F192I 100 169 T169H/F192I/D203Q 86 170 T169H/F192I/D203N 97 171 T148A/D152N/D154N/T169H/F192I 95 172 T148A/D154N/T69H/F192I 87 173 D166Q/S171Q/F192I 104 174 D166N/S171Q/F192I 97 175 S171Q/D186Q/F192I 126 176 S171Q/D186N/F192I 116 177 S171Q/F192I/D203Q 90 178 S171Q/F192I/D203N 90 179 T148A/D152N/D154N/S171Q/F192I ND 180 T148A/D154N/S171Q/F192I 104 181 D166Q/S174Q/F192I 93 182 D166N/S174Q/F192I 95 183 S174Q/D186Q/F192I 129 184 S174Q/D186N/F192I 109 185 S174Q/F192I/D203Q 95 186 S174Q/F192I/D203N 96 187 T148A/D152N/D154N/S171Q/F192I 97 188 T148A/D154N/S171Q/F192I 91 189 D166Q/S174H/F192I 93 190 D166N/S174H/F192I 102 191 S174H/D186Q/F192I 110 192 S174H/D186N/F192I 102 193 S174H/F192I/D203Q 98 194 S174H/F192I/D203N 99 195 T148A/D152N/D154N/S174H/F192I 98 196 T148A/D154N/S174H/F192I 102 197 D166Q/T179Q/F192I 100 198 D166N/T179Q/F192I 89 199 T179Q/D186Q/F192I 120 200 T179Q/D186N/F192I 107 201 T179Q/F192I/D203Q 92 202 T179Q/F192I/D203N 94 203 T148A/D152N/D154N/T179Q/F192I 106 204 T148A/D154N/T179Q/F192I 98 205 D166Q/T179H/F192I 103 206 D166N/T179H/F192I 97 207 T179H/D186Q/F192I 130 208 T179H/D186N/F192I 113 209 T179H/F192I/D203Q 94 210 T179H/F192I/D203N 96 211 T148A/D152N/D154N/T179H/F192I 103 212 T148A/D154N/T179H/F192I 102

Resistance to proteolysis of FIX SuperLEADs was assayed as described above in Example 4. For testing of FIX SuperLEADs, the concentration of selected proteases (trypsin, chymotrypsin, endoproteinase AspN, endoproteinase GluC, and elastase) was increased to 6% w/w. Resistance to proteases for exemplary non-limiting modified FIX SuperLEAD polypeptides is displayed in Table 15a. The data is expressed as relative resistance to proteases among the samples tested: (+), (++), or (+++), with (+++) indicating the highest resistance to proteases.

TABLE 15a Resistance to proteolysis of FIX SuperLEAD mutant proteins Nemo Resistance Code # Mutation to proteases 107 T163H/F192I (+) 108 I164Q/F192I (+) 109 T163N/I164N/F192I (+) 110 T169H/F192I (+) 111 S171Q/F192I (+) 112 S174Q/F192I (+) 113 S174H/F192I (+) 114 T179Q/F192I (+) 115 T179H/F192I (+) 116 D166Q/F192I (+) 117 D166N/F192I (+) 118 D186Q/F192I (++) 119 D186N/F192I (+) 120 F192I/D203Q (+) 121 F192I/D203N (+) 122 T148A/D152N/D154N/ (++) F192I 123 T148A/D154N/F192I (+) 141 T163H/D166Q/F192I (++) 142 T163H/D166N/F192I (+) 143 T163H/D186Q/F192I (+) 144 T163H/D186N/F192I (+) 145 T163H/F192I/D203Q (++) 146 T163H/F192I/D203N (+) 147 T148A/D152N/D154N/ (+) T163H/F192I 148 T148A/D154N/T163H/ (++) F192I 149 I164Q/D166Q/F192I (+) 150 I164Q/D166N/F192I (+) 151 I164Q/D186Q/F192I (+) 152 I164Q/D186N/F192I (+) 153 I164Q/F192I/D203Q (++) 154 I164Q/F192I/D203N (++) 155 T148A/D152N/D154N/ (+) I164Q/F192I 156 T148A/D154N/I164Q/ (+) F192I 157 T163N/I164N/D166Q/ (+) F192I 158 T163N/I164N/D166N/ (+) F192I 159 T163N/I164N/D186Q/ (+) F192I 160 T163N/I164N/D186N/ (+) F192I 161 T163N/I164N/F192I/ (+) D203Q 162 T163N/I164N/F192I/ (+) D203N 163 T148A/D152N/D154N/ (+) T163N/I164N/F192I 164 T148A/D154N/T163N/ (++) I164N/F192I 165 D166Q/T169H/F192I (+) 166 D166N/T169H/F192I (+) 167 T169H/D186Q/F192I (+) 168 T169H/D186N/F192I (+) 169 T169H/F192I/D203Q (+) 170 T169H/F192I/D203N (++) 171 T148A/D152N/D154N/ (+) T169H/F192I 172 T148A/D154N/T169H/F192I (+) 173 D166Q/S171Q/F192I (+) 174 D166N/S171Q/F192I (+) 175 S171Q/D186Q/F192I (+) 176 S171Q/D186N/F192I (+) 177 S171Q/F192I/D203Q (+) 178 S171Q/F192I/D203N (+) 179 T148A/D152N/D154N/ (+) S171Q/F192I 180 T148A/D154N/S171Q/F192I (+) 181 D166Q/S174Q/F192I (+) 182 D166N/S174Q/F192I (+) 183 S174Q/D186Q/F192I (+) 184 S174Q/D186N/F192I (+) 185 S174Q/F192I/D203Q (+++) 186 S174Q/F192I/D203N (+) 187 T148A/D152N/D154N/ (+) S174Q/F192I 188 T148A/D154N/S174Q/F192I (+) 189 D166Q/S174H/F192I (+) 190 D166N/S174H/F192I (+) 191 S174H/D186Q/F192I (+) 192 S174H/D186N/F192I (+++) 193 S174H/F192I/D203Q (+) 194 S174H/F192I/D203N (+) 195 T148A/D152N/D154N/ (+) S174H/F192I 196 T148A/D154N/S174H/F192I (+) 197 D166Q/T179Q/F192I (+) 198 D166N/T179Q/F192I (+) 199 T179Q/D186Q/F192I (+) 200 T179Q/D186N/F192I (+) 201 T179Q/F192I/D203Q (+++) 202 T179Q/F192I/D203N (+) 203 T148A/D152N/D154N/ (+) T179Q/F192I 204 T148A/D154N/T179Q/F192I (+) 205 D166Q/T179H/F192I (+) 206 D166N/T179H/F192I (+) 207 T179H/D186Q/F192I (+) 208 T179H/D186N/F192I (+) 209 T179H/F192I/D203Q (+) 210 T179H/F192I/D203N (+) 211 T148A/D152N/D154N/ (+) T179H/F192I 212 T148A/D154N/T179H/F192I (+)

All variants tested exhibited increased protease resistance relative to the native FIX polypeptide. Several FIX SuperLEAD polypeptides exhibited particularly high resistance to proteases including D186Q/F 192I, Ti 48A/D 152N/D 154N/F 192I, T163H/D166Q/F192I, T163H/F192I/D203Q, T148A/D154N/T163H/F192I, I164Q/F192I/D203 Q, I164Q/F192I/D203N, T148A/D154N/T163N/I164N/F192I, T169H/F 192I/D203N, S174Q/F192I/D203Q, S174H/D186N/F192I, and T179Q/F192I/D203 Q.

In a separate experiment, protease resistance of selected SuperLEADs was assayed by the same methods as described above. In this experiment, the data for resistance to proteases was compared in terms of t_(1/2) clotting time fold increase at 50% of T₀ compared to native Factor IX. Data for this analysis is shown in Table 15b.

TABLE 15b Resistance to proteolysis of FIX SuperLEAD mutant proteins protease resistance Nemo protease specificity clotting time (50% t_(1/2) clotting fold- code mutations of leads (seconds) increase versus native) 161 T163N/I164N/F192I/D203Q EndAsp + CT + E 101 4.2 194 S174H/F192I/D203N EndAsp + CT + E 99 4.2 195 T148A/D152N/D154N/S174H/F192I EndAsp + CT + E 98 4 145 T163H/F192I/D203Q EndAsp + CT + E 90 3.3 107 F192I-T163H EndAsp + CT 99 3.2 120 F192I-D203Q EndAsp + CT 90 3.2 147 T148A/D152N/D154N/T163H/F192I EndAsp + CT + E 101 3 170 T169H/F192I/D203N EndAsp + CT + E 97 2.8 177 S171Q/F192I/D203Q EndAsp + CT + E 90 2.8 203 T148A/D152N/D154N/T179Q/F192I EndAsp + CT + E 106 2.8 153 I164Q/F192I/D203Q EndAsp + CT + E 96 2.7 196 T148A/D154N/S174H/F192I EndAsp + CT + E 102 2.7 157 T163N/I164N/D166Q/F192I EndAsp + CT + E 103 2.5 180 T148A/D154N/S171Q/F192I EndAsp + CT + E 104 2.5 193 S174H/F192I/D203Q EndAsp + CT + E 98 2.5 204 T148A/D154N/T179Q/F192I EndAsp + CT + E 98 2.5 146 T163H/F192I/D203N EndAsp + CT + E 89 2.3 169 T169H/F192I/D203Q EndAsp + CT + E 86 2.3 179 T148A/D152N/D154N/S171Q/F192I EndAsp + CT + E 97 2.3 192 S174H/D186N/F192I EndAsp + CT + E 102 2.3 172 T148A/D154N/T169H/F192I EndAsp + CT + E 87 2.2 173 D166Q/S171Q/F192I EndAsp + CT + E 104 2.2 202 T179Q/F192I/D203N EndAsp + CT + E 94 2.2 185 S174Q/F192I/D203Q EndAsp + CT + E 95 2 187 T148A/D152N/D154N/S174Q/F192I EndAsp + CT + E 97 1.8 190 D166N/S174H/F192I EndAsp + CT + E 102 1.8 119 F192I-D186N EndAsp + CT 111 1.7 205 D166Q/T179H/F192I EndAsp + CT + E 103 1.7 148 T148A/D154N/T163H/F192I EndAsp + CT + E 92 1.5 175 S171Q/D186Q/F192I EndAsp + CT + E 126 1.5 155 T148A/D152N/D154N/I164Q/F192I EndAsp + CT + E 97 1.3 native FIX 114 1

All variants tested exhibited increased protease resistance relative to the native FIX polypeptide. Exemplary FIX SuperLEAD polypeptides that exhibited particularly high resistance to proteases in this analysis included T163N/I164N/F192I/D203Q, S174H/F192I/D203N, T148A/D152N/D154N/S174H/F192I, T163H/F192I/D203Q, T163H/F192I, F192I/D203Q, T148A/D152N/D154N/T163H/F192I, T169H/F192I/D203N, S171Q/F192I/D203Q, and T148A/D152N/D154N/T179Q/F192I.

The data above for the protease resistance are exemplary showing the resistance to proteolysis to an exemplary protease cocktail containing the proteases as described above. Thus, the data are not comprehensive and are not meant to be indicative that other FIX polypeptides do not exhibit protease resistance.

Example 6 SuperLEAD Clotting Activity and Resistance to Proteolysis Using an Alternative FIX Polypeptide Background

As mentioned in Example 1, the starting FIX polypeptide on which the FIX variants were generated is shown in SEQ ID NO: 1035. This sequence differs from another wild-type FIX polypeptide shown in SEQ ID NO: 2 at five positions: K39T, L40E, I43K, S44Q and S46V. These changes, however, do not affect the clotting activity of the FIX polypeptide. In order to compare the activity of the FIX variants between the two polypeptide backgrounds, site-directed mutagenesis was performed to convert the SuperLEAD variants to the alternative FIX background (BFIX-T148). The mutants that were generated are shown in Table 16.

TABLE 16 FIX SuperLEAD Variants Produced on BFIX-T148 Background NFIX code BFIX-T148 code mutations 161 249 T163N/I164N/F192I/D203Q 194 250 S174H/F192I/D203N 195 251 T148A/D152N/D154N/S174H/F192I 145 252 T163H/F192I/D203Q 107 253 T163H/F192I 120 254 F192I/D203Q 147 255 T148A/D152N/D154N/T163H/F192I 170 256 T169H/F192I/D203N 177 257 S171Q/F192I/D203Q 203 258 T148A/D152N/D154N/T179Q/F192I 153 259 I164Q/F192I/D203Q 196 260 T148A/D154N/S174H/F192I 157 261 T163N/I164N/D166Q/F192I 180 262 T148A/D154N/S171Q/F192I 193 263 S174H/F192I/D203Q 204 264 T148A/D154N/T179Q/F192I 146 265 T163H/F192I/D203N 169 266 T169H/F192I/D203Q 179 267 T148A/D152N/D154N/S171Q/F192I 192 268 S174H/D186N/F192I 172 269 T148A/D154N/T169H/F192I 173 270 D166Q/S171Q/F192I 202 271 T179Q/F192I/D203N 185 272 S174Q/F192I/D203Q 187 273 T148A/D152N/D154N/S174Q/F192I 190 274 D166N/S174H/F192I 119 275 D186N/F192I 205 276 D166Q/T179H/F192I 148 277 T148A/D154N/T163H/F192I 175 278 S171Q/D186Q/F192I 155 279 T148A/D152N/D154N/I164Q/F192I

Human fetal kidney 293 HEK EBNA fibroblast cell line was grown in Dulbecco's modified eagle medium supplemented with 2 mM of glutamine and 10% of fetal bovine serum (FBS). Cells were plated at 5×10⁵ cells per well in 6-well plates for 2 days, washed twice with PBS and then placed in serum-free medium. Cells were transfected with 2 μg of DNA using transfection reagent (PEI, NaCl). The cell medium was replaced after 4 hours by serum-free medium containing 50 μg/mL of K vitamin and 1×-ITS (Insulin, Transferrin, Selenium) mixture. The cell medium was collected 72 h after transfection and stored at −80° C.

Asserachrom® IX:Ag Elisa kit (Diagnostica Stago, France) was used to determine the concentration of the 31 selected mutant cell productions according to the instructions of the manufacturer. Samples were diluted 20-fold using the dilution reagent. Absorbance at 492 nm was measured using a spectrophotometer (Spectramax, Molecular Devices). Results were obtained by interpolation of the absorbance values from the calibration curve obtained from patients' plasma dilutions and plotted in a log-log graph. Factor IX level at 100% corresponds approximately to 4 mg/L. Data are presented in Table 17.

TABLE 17 Yields for BFIX T148 Super LEAD variants.

Mean of production corresponds to 3 separated productions (except for mutants marked with * = only one production). Lower produced mutants are highlighted in grey.

In order to determine the bioactivity of each mutant, the clotting activity was measured by the one-stage activated partial thromboplastin time (aPTT) clotting assay (Cephascreen, Diagnostica Stago, France) using Factor IX immunodepleted human plasma (Deficient IX, Diagnostica Stago, France). Supernatants containing 60 ng of native or mutant Factor IX molecules from transient transfection production were diluted with 60 μL of immunodepleted plasma. 80 μL of Cephascreen reagent containing cephalin (platelet substitute) prepared from rabbit cerebral tissues and a polyphenolic activator in a buffered medium was added to dilute Factor IX samples and incubated at 37° C. for 15 minutes. Thus, 80 μL of pre-warmed CaCl₂ (0.025M, Diagnostica Stago, France) was added to Factor IX samples/Cephascreen reagent mix. The time required for clot formation was immediately monitored using a spectrophotometer (Spectramax, Molecular devices) at 350 nm. A serial dilution of normal human pooled plasma representing 100 to 120% of Factor IX activity (System control N, Diagnostica Stago, France) was used as the standard curve in order to validate the linearity of the clotting time detection. Data are presented in Table 18.

TABLE 18 Clotting activity of BFIX T148 SuperLEAD variants mutant number Production 1 Production 2 Production 3 MEAN OF T50 in BFIX-T148 T50 (clotting) conversion T50 (clotting) conversion T50 (clotting) conversion (clotting) Rank matrix (seconds) (μg/l) (seconds) (μg/l) (seconds) (μg/l) (seconds) 1 249 122 38.2 100 46.7 110 22.9 111 2 250 121 34.0 114 24.0 99 40.2 111 3 251 131 21.2 132 10.7 99 40.2 121 4 252 105 33.5 122 18.7 106 43.9 111 5 253 113 22.8 128 13.8 136 12.4 125 6 254 114 21.7 128 13.4 130 15.6 124 7 255 137 18.9 103 39.1 110 23.9 117 8 256 140 17.1 107 32.4 108 26.2 118 9 257 nd nd nd nd 114 30.4  114* 10 258 121 32.2 116 24.1 98 42.5 112 11 259 nd nd 109 29.6 130 15.7 119 12 260 128 23.4 120 17.9 101 36.7 117 13 261 144 14.9 115 21.8 110 23.1 123 14 262 nd nd nd nd 133 13.9  133* 15 263 118 23.3 100 51.3 115 18.7 111 16 264 118 37.7 108 34.9 109 39.2 111 17 265 nd nd 106 34.1 120 23.0 113 18 266 138 19.6 115 21.5 100 39.6 118 19 267 115 21.3 123 16.7 128 16.5 122 20 268 nd nd nd nd 126 18.5  126* 21 269 115 24.9 110 28.8 105 30.5 110 22 270 120 19.8 118 19.8 116 17.5 118 23 271 133 11.4 106 34.2 115 18.1 118 24 272 125 15.5 116 21.8 120 14.9 120 25 273 nd nd 125 14.6 128 16.8 126 26 274 118 21.7 102 45.3 109 24.4 109 27 275 nd nd 135 10.5 147 8.1 141 28 276 nd nd 123 17.1 135 12.9 129 29 277 127 14.8 116 21.6 102 34.5 115 30 278 136 17.8 129 12.6 135 12.6 133 31 279 128 28.4 102 39.9 113 20.7 114 BFIX 107 48  103 44  105 BFIX-T148 116 32  104 42  120 15.0 113 NFIX 128 19  117 21  123 Mean of production corresponds to 3 separated clotting time assays (except for mutants marked with * = only one production). Conversion in μg/L was based from standard curves obtained from normal human sera.

All selected mutants in BFIX-T148 background were active by clotting time assays and were similar to BFIX-T148 native sequence (t_(1/2) between 111 sec and 133 sec). Only mutant 275 exhibited a clotting time higher than 140 sec.

Since modifications will be apparent to those of skill in this art, it is intended that this invention be limited only by the scope of the appended claims. 

What is claimed is:
 1. A modified factor IX (FIX) polypeptide, comprising an amino acid replacement that corresponds to one or more amino acid replacements selected from among E410N, K247N and K228N in the FIX polypeptide set forth in SEQ ID NO: 2 or 1035, wherein: corresponding residues are identified by alignment; the modified FIX polypeptide comprises a sequence of amino acid residues that is at least 90% identical to a polypeptide with an amino acid sequence selected from among the sequences set forth in SEQ ID NOs: 2, 892, 893, 898-912 and 1035; and the modified FIX polypeptide retains coagulant activity.
 2. The modified FIX polypeptide of claim 1, wherein the FIX polypeptide comprises an amino acid replacement at a position corresponding to an amino acid position selected from among Y1, S3, G4, K5, L6, E7, E8, F9, V10, G12, L14, E15, R16, E17, M19, E20, E21, K22, S24, F25, E26, E27, A28, R29, E30, V31, F32, E33, T35, T38, F41, W42, K43, Y45, V46, D47, G48, D49, E52, S53, P55, L57, N58, G59, G60, K63, D64, D65, I66, Y69, W72, F75, G76, F77, E78, G79, E83, L84, V86, I90, K91, N92, G93, R94, E96, F98, K100, A103, D104, K106, V107, V108, S110, T112, E113, G114, Y115, R116, L117, A118, S123, A127, V128, P131, G133, V135, V137, S138, T140, S141, K142, L143, R145, A146, T148, V149, D152, V153, D154, Y155, V156, S158, T159, E160, A161, E162, T163, I164, L165, I168, F175, F178, T179, R180, V181, V182, G183, G184, E185, D186, A187, K188, P189, G190, F192, P193, W194, V196, V197, L198, N199, G200, K201, V202, D203, A204, F205, G207, G208, S209, I210, V211, E213, K214, W215, I216, V217, T218, A219, A220, V223, G226, V227, K228, I229, T230, V231, V232, A233, G234, E235, I238, E239, E240, E245, R248, V250, I251, R252, I253, I254, P255, Y259, A261, A262, I263, K265, Y266, D269, I270, A271, L272, L273, E274, L275, D276, E277, P278, L279, V280, L281, S283, Y284, V285, T286, P287, I288, I290, A291, D292, K293, Y295, T296, I298, F299, L300, K301, F302, G303, S304, G305, Y306, V307, S308, G309, W310, G311, R312, V313, F314, K316, G317, R318, S319, A320, L321, V322, L323, Y325, L326, R327, V328, P329, L330, V331, D332, R333, A334, T335, L337, R338, S339, T340, K341, F342, T343, I344, Y345, M348, F349, A351, G352, F353, E355, G356, G357, R358, D359, S360, G363, D364, S365, G366, G367, P368, V370, V373, E374, G375, T376, S377, F378, L379, T380, G381, I382, I383, S384, W385, G386, E387, E388, A390, M391, K392, G393, K394, Y395, G396, I397, Y398, T399, K400, V401, S402, R403, Y404, V405, W407, I408, K409, E410, K411, T412, K413, and T415 of the FIX polypeptide set forth in SEQ ID NO: 2 or
 1035. 3. The modified FIX polypeptide of claim 2, wherein: the amino acid replacement corresponds to a replacement selected from among Y1H, Y1I, S3Q, S3H, S3N, G4Q, G4H, G4N, K5N, K5Q, L6I, L6V, E7Q, E7H, E7N, E8Q, E8H, E8N, F9I, F9V, V10Q, V10H, V10N, G12Q, G12H, G12N, L14I, L14V, E15Q, E15H, E15N, R16H, R16Q, E17Q, E17H, E17N, M191, M19V, E20Q, E20H, E20N, E21Q, E21H, E21N, K22N, K22Q, S24Q, S24H, S24N, F251, F25V, E26Q, E26H, E26N, E27Q, E27H, E27N, A28Q, A28H, A28N, R29H, R29Q, E30Q, E30H, E30N, V31Q, V31H, V31N, F32I, F32V, E33Q, E33H, E33N, T35Q, T35H, T35N, T38Q, T38H, T38N, F41I, F41V, W42S, W42H, K43N, K43Q, Y45H, Y451, V46Q, V46H, V46N, D47N, D47Q, G48Q, G48H, G48N, D49N, D49Q, E52Q, E52H, E52N, S53Q, S53H, S53N, P55A, P55S, L57I, L57V, N58Q, N58S, G59Q, G59H, G59N, G60Q, G60H, G60N, K63N, K63Q, D64N, D64Q, D65N, D65Q, 166Q, 166H, 166N, Y69H, Y69I, W72S, W72H, F75I, F75V, G76Q, G76H, G76N, F771, F77V, E78Q, E78H, E78N, G79Q, G79H, G79N, E83Q, E83H, E83N, L84I, L84V, V86Q, V86H, V86N, 190Q, 190H, 190N, K91N, K91Q, N92Q, N92S, G93Q, G93H, G93N, R94H, R94Q, E96Q, E96H, E96N, F98I, F98V, K100N, K100Q, A103Q, A103H, A103N, D104N, D104Q, K106N, K106Q, V107Q, V107H, V107N, V108Q, V108H, V108N, S110Q, S110H, S110N, T112Q, T112H, T112N, E113Q, E113H, E113N, G114Q, G114H, G114N, Y115H, Y115I, R116H, R116Q, L117I, L117V, A118Q, A118H, A118N, S123Q, S123H, S123N, A127Q, A127H, A127N, V128Q, V128H, V128N, P131A, P131S, G133Q, G133H, G133N, V135Q, V135H, V135N, V137Q, V137H, V137N, S138Q, S138H, S138N, T140Q, T140H, T140N, S141Q, S141H, S141N, K142N, K142Q, L143I, L143V, R145H, R145Q, A146Q, A146H, A146N, T148Q, T148H, T148N, V149Q, V149H, V149N, D152N, D152Q, V153Q, V153H, V153N, D154N, D154Q, Y155H, Y155I, V156Q, V156H, V156N, S158Q, S158H, S158N, T159Q, T159H, T159N, E160Q, E160H, E160N, A161Q, A161H, A161N, E162Q, E162H, E162N, T163Q, T163H, T163N, I164Q, I164H, I164N, L165I, L165V, L165Q, L165H, I168Q, I168H, I168N, F175I, F175V, F175H, F178I, F178V, F178H, T179Q, T179H, T179N, R180H, R180Q, V181Q, V181H, V181N, V182Q, V182H, V182N, G183Q, G183H, G183N, G184Q, G184H, G184N, E185Q, E185H, E185N, D186N, D186Q, A187Q, A187H, A187N, K188N, K188Q, P189A, P189S, G190Q, G190H, G190N, F192I, F192V, F192H, P193A, P193S, W194S, W194H, W194I, V196Q, V196H, V196N, V197Q, V197H, V197N, L198I, L198V, L198Q, L198H, N199Q, N199S, G200Q, G200H, G200N, K201N, K201Q, V202Q, V202H, V202N, D203N, D203Q, A204Q, A204H, A204N, F205I, F205V, G207Q, G207H, G207N, G208Q, G208H, G208N, S209Q, S209H, S209N, I210Q, I210H, I210N, V211Q, V211H, V211N, E213Q, E213H, E213N, K214N, K214Q, W215S, W215H, I216Q, I216H, I216N, V217Q, V217H, V217N, T218Q, T218H, T218N, A219Q, A219H, A219N, A220Q, A220H, A220N, V223Q, V223H, V223N, G226Q, G226H, G226N, V227Q, V227H, V227N, K228N, K228Q, I229Q, I229H, I229N, T230Q, T230H, T230N, V231Q, V231H, V231N, V232Q, V232H, V232N, A233Q, A233H, A233N, G234Q, G234H, G234N, E235Q, E235H, E235N, I238Q, I238H, I238N, E239Q, E239H, E239N, E240Q, E240H, E240N, E245Q, E245H, E245N, R248H, R248Q, V250Q, V250H, V250N, I251Q, I251H, I251N, R252H, R252Q, I253Q, I253H, I253N, I254Q, I254H, I254N, P255A, P255S, Y259H, Y259I, A261Q, A261H, A261N, A262Q, A262H, A262N, I263Q, I263H, I263N, K265N, K265Q, Y266H, Y266I, D269N, D269Q, I270Q, I270H, I270N, A271Q, A271H, A271N, L272I, L272V, L273I, L273V, E274Q, E274H, E274N, L275I, L275V, D276N, D276Q, E277Q, E277H, E277N, P278A, P278S, L279I, L279V, V280Q, V280H, V280N, L281I, L281V, S283Q, S283H, S283N, Y284H, Y284I, V285Q, V285H, V285N, T286Q, T286H, T286N, P287A, P287S, I288Q, I288H, I288N, I290Q, I290H, I290N, A291Q, A291H, A291N, D292N, D292Q, K293N, K293Q, Y295H, Y295I, T296Q, T296H, T296N, I298Q, I298H, I298N, F299I, F299V, L300I, L300V, K301N, K301Q, F302I, F302V, G303Q, G303H, G303N, S304Q, S304H, S304N, G305Q, G305H, G305N, Y306H, Y306I, V307Q, V307H, V307N, S308Q, S308H, S308N, G309Q, G309H, G309N, W310S, W310H, G311Q, G311H, G311N, R312H, R312Q, V313Q, V313H, V313N, F314I, F314V, K316N, K316Q, G317Q, G317H, G317N, R318H, R318Q, S319Q, S319H, S319N, A320Q, A320H, A320N, L321I, L321V, V322Q, V322H, V322N, L323I, L323V, Y325H, Y325I, L326I, L326V, R327H, R327Q, V328Q, V328H, V328N, P329A, P329S, L330I, L330V, V331Q, V331H, V331N, D332N, D332Q, R333H, R333Q, A334Q, A334H, A334N, T335Q, T335H, T335N, L337I, L337V, R338H, R338Q, S339Q, S339H, S339N, T340Q, T340H, T340N, K341N, K341Q, F342I, F342V, T343Q, T343H, T343N, I344Q, I344H, I344N, Y345H, Y345I, M348I, M348V, F349I, F349V, A351Q, A351H, A351N, G352Q, G352H, G352N, F353I, F353V, E355Q, E355H, E355N, G356Q, G356H, G356N, G357Q, G357H, G357N, R358H, R358Q, D359N, D359Q, S360Q, S360H, S360N, G363Q, G363H, G363N, D364N, D364Q, S365Q, S365H, S365N, G366Q, G366H, G366N, G367Q, G367H, G367N, P368A, P368S, V370Q, V370H, V370N, V373Q, V373H, V373N, E374Q, E374H, E374N, G375Q, G375H, G375N, T376Q, T376H, T376N, S377Q, S377H, S377N, F378I, F378V, L379I, L379V, T380Q, T380H, T380N, G381Q, G381H, G381N, I382Q, I382H, I382N, I383Q, I383H, I383N, S384Q, S384H, S384N, W385S, W385H, G386Q, G386H, G386N, E387Q, E38711, E387N, E388Q, E388H, E388N, A390Q, A390H, A390N, M391I, M391V, K392N, K392Q, G393Q, G393H, G393N, K394N, K394Q, Y395H, Y395I, G396Q, G396H, G396N, I397Q, I397H, I397N, Y398H, Y398I, T399Q, T399H, T399N, K400N, K400Q, V401Q, V401H, V401N, S402Q, S402H, S402N, R403H, R403Q, Y404H, Y404I, V405Q, V405H, V405N, W407S, W407H, I408Q, I408H, I408N, K409N, K409Q, E410Q, E410H, E410N, K411N, K411Q, T412Q, T412H, T412N, K413N, K413Q, T415Q, T415H, and T415N of the FIX polypeptide set forth in SEQ ID NO: 2 or
 1035. 4. The modified FIX polypeptide of claim 1, wherein the unmodified FIX polypeptide has a sequence of amino acids set forth in SEQ ID NO:
 2. 5. The modified FIX polypeptide of claim 1, wherein the unmodified FIX polypeptide has a sequence of amino acids set forth in SEQ ID NO:
 1035. 6. The modified FIX polypeptide of claim 1, comprising the sequence of amino acids set forth in one of SEQ ID NOs: 225, 242, 396, 1274, 1257 and
 1428. 7. The modified FIX polypeptide of claim 1, wherein the unmodified FIX polypeptide is a human polypeptide.
 8. The modified FIX polypeptide of claim 1, wherein the unmodified FIX polypeptide is a non-human polypeptide.
 9. The modified FIX polypeptide of claim 1, wherein the modified FIX polypeptide comprises 2, 3, 4, or 5 amino acid replacements compared to the unmodified polypeptide, wherein the unmodified polypeptide comprises the sequence of amino acids set forth in SEQ ID NO: 2 or
 1035. 10. The modified FIX polypeptide of claim 1, wherein the polypeptide is a naked polypeptide chain.
 11. The modified FIX polypeptide of claim 1, wherein the modified FIX polypeptide is glycosylated, carboxylated, hydroxylated, sulfated, phosphorylated, albuminated, or conjugated to a polyethylene glycol (PEG) moiety.
 12. The modified FIX polypeptide of claim 1, comprising an amino acid modification that contributes to an altered property selected from among glycosylation, carboxylation, hydroxylation, sulfation, phosphorylation, PEGylation and a modification to decrease immunogenicity upon administration to a human.
 13. The modified FIX polypeptide of claim 2, wherein the amino acid replacement is selected from among natural amino acids, non-natural amino acids and a combination of natural and non-natural amino acids.
 14. The modified FIX polypeptide of claim 1, wherein the modified FIX polypeptide is a mature polypeptide.
 15. The modified FIX polypeptide of claim 1, wherein the modified FIX polypeptide is a precursor polypeptide.
 16. The modified FIX polypeptide of claim 15, wherein the modified FIX polypeptide comprises a signal peptide.
 17. The modified FIX polypeptide of claim 1, wherein the modified FIX polypeptide lacks a signal peptide.
 18. The modified FIX polypeptide of claim 1, wherein the modified FIX polypeptide comprises a propeptide.
 19. The modified FIX polypeptide of claim 1, wherein the modified FIX polypeptide lacks a propeptide.
 20. The modified FIX polypeptide of claim 1, wherein the modified FIX polypeptide is a zymogen.
 21. The modified FIX polypeptide of claim 1, wherein the modified FIX polypeptide is an activated FIX polypeptide.
 22. The modified FIX polypeptide of claim 1, wherein the modified FIX polypeptide is secreted.
 23. The modified FIX polypeptide of claim 1, wherein the modified FIX polypeptide comprises a heavy chain and/or a light chain.
 24. The modified FIX polypeptide of claim 1, comprising the sequence of amino acids set forth in SEQ ID NO: 242 or 1274, and optionally additional amino acid replacements.
 25. The modified FIX polypeptide of claim 1, comprising the sequence of amino acids set forth in SEQ ID NO: 225 or 1257, and optionally additional amino acid replacements.
 26. The modified FIX polypeptide of claim 1, comprising the sequence of amino acids set forth in SEQ ID NO: 396 or 1428, and optionally additional amino acid replacements.
 27. A pharmaceutical composition, comprising the modified FIX polypeptide of claim
 1. 28. The pharmaceutical composition of claim 27, wherein the pharmaceutical composition is formulated for local, systemic or topical administration.
 29. The pharmaceutical composition of claim 28 that is formulated for oral, nasal, pulmonary, buccal, transdermal, subcutaneous, intraduodenal, enteral, parenteral, intravenous, or intramuscular administration.
 30. The pharmaceutical composition of claim 28 that is formulated for oral administration.
 31. The pharmaceutical composition of claim 27, wherein the modified FIX polypeptide is glycosylated, carboxylated, hydroxylated, sulfated, phosphorylated, albuminated, or conjugated to a polyethylene glycol (PEG) moiety.
 32. The pharmaceutical composition of claim 27, wherein the polypeptide comprises an amino acid modification that decreases immunogenicity upon administration to a human compared to the polypeptide that does not comprise the amino acid modification.
 33. The pharmaceutical composition of claim 27, wherein an amino acid modification comprises a substitution with a natural amino acids, a substitution with a non-natural amino acids or combinations thereof.
 34. The pharmaceutical composition of claim 27 that is formulated for administration in a form selected from among a liquid, a pill, a tablet, a lozenge and a capsule.
 35. The pharmaceutical composition of claim 34, wherein the tablet or capsule is enterically coated.
 36. The pharmaceutical composition of claim 27 that is formulated for controlled-release of the modified FIX polypeptide.
 37. The pharmaceutical composition of claim 34, wherein the pill, tablet, lozenge, or capsule delivers the modified FIX polypeptide to the mucosa of the mouth, throat, or gastrointestinal tract.
 38. A method, comprising treating a subject by administering the pharmaceutical composition of claim 27, wherein the subject has a disease or condition that is treated by administration of FIX.
 39. The method of claim 38, wherein the disease or condition is treated by administration of inactive FIX or active FIX.
 40. The method of claim 38, wherein the disease or condition to be treated is selected from among hemophilia, thrombotic disease, and hemorrhagic disease.
 41. The method of claim 38, wherein the condition to be treated is disseminated intravascular coagulation (DIC).
 42. The method of claim 40, wherein the disease or condition is hemophilia B.
 43. The method of claim 40, wherein the disease or conditions is hemophilia that is congenital.
 44. The method of claim 40, wherein the disease is hemophilia that is acquired.
 45. The method of claim 40, wherein disease or conditions is a thrombotic disease or hemorrhagic disease selected from among ischemia, stroke, atherosclerosis, antithrombin III deficiency and protein C deficiency.
 46. The modified FIX polypeptide of claim 1, wherein the mature form thereof comprises a sequence of amino acid residues that is at least 95% identical to a polypeptide with an amino acid sequence selected from among a mature form of a FIX polypeptide with the sequence set forth in any of SEQ ID NOs: 2, 892, 893, 898-912 and
 1035. 